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Conserved domains on  [gi|73535323|pdb|1U3S|A]
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Chain A, Estrogen receptor beta

Protein Classification

nuclear hormone receptor family protein( domain architecture ID 10161265)

nuclear hormone receptor family protein is a ligand-regulated transcriptional modulator that may play a role in many developmental processes; similar to Rattus norvegicus nuclear receptor subfamily 0 group B member 2

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NR_LBD_ER cd06949
Ligand binding domain of Estrogen receptor, which are activated by the hormone ...
 3-238 4.92e-130

Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen); The ligand binding domain (LBD) of Estrogen receptor (ER): Estrogen receptor, a member of nuclear receptor superfamily, is activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The C-terminal LBD also contains AF-2 activation motif, the dimerization motif, and part of the nuclear localization region. Estrogen receptor has been linked to aging, cancer, obesity and other diseases.


:

Pssm-ID: 132747  Cd Length: 235  Bit Score: 366.75  E-value: 4.92e-130
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A        3 LSPEQLVLTLLEAEPPHVLISR-PSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMM 81
Cdd:cd06949   1 LSAEQLISALLEAEPPHIYSEYdPTRPFTEASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLML 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       82 GLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVtaTQDAD 161
Cdd:cd06949  81 GLVWRSMEHPGKLLFAPDLLLDRNQGSCVEGMVEIFDMLLATASRFRELQLQREEYVCLKAIILLNSSVYTFL--LESLE 158

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
1U3S_A      162 SSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAH 238
Cdd:cd06949 159 SRRQVQRLLDKITDALVHACSKRGLSLQQQSRRLAQLLLILSHIRHVSNKGMEHLYSMKCKNVVPLYDLLLEMLDAH 235
 
Name Accession Description Interval E-value
NR_LBD_ER cd06949
Ligand binding domain of Estrogen receptor, which are activated by the hormone ...
 3-238 4.92e-130

Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen); The ligand binding domain (LBD) of Estrogen receptor (ER): Estrogen receptor, a member of nuclear receptor superfamily, is activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The C-terminal LBD also contains AF-2 activation motif, the dimerization motif, and part of the nuclear localization region. Estrogen receptor has been linked to aging, cancer, obesity and other diseases.


Pssm-ID: 132747  Cd Length: 235  Bit Score: 366.75  E-value: 4.92e-130
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A        3 LSPEQLVLTLLEAEPPHVLISR-PSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMM 81
Cdd:cd06949   1 LSAEQLISALLEAEPPHIYSEYdPTRPFTEASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLML 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       82 GLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVtaTQDAD 161
Cdd:cd06949  81 GLVWRSMEHPGKLLFAPDLLLDRNQGSCVEGMVEIFDMLLATASRFRELQLQREEYVCLKAIILLNSSVYTFL--LESLE 158

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
1U3S_A      162 SSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAH 238
Cdd:cd06949 159 SRRQVQRLLDKITDALVHACSKRGLSLQQQSRRLAQLLLILSHIRHVSNKGMEHLYSMKCKNVVPLYDLLLEMLDAH 235
HOLI smart00430
Ligand binding domain of hormone receptors;
42-208 2.36e-26

Ligand binding domain of hormone receptors;


Pssm-ID: 214658  Cd Length: 163  Bit Score: 100.13  E-value: 2.36e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A          42 ADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGIL---EIFD 118
Cdd:smart00430   1 AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAPDGTYIRPDAVLELRKLfspFLDR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A         119 MLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQdadssRKLAHLLNAVTDALVWVIAKSGisSQQQSMRLANL 198
Cdd:smart00430  81 ILSELVKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGK-----EIVEKLQEKYANALHDYYLKNY--PMNYPGRFAKL 153

                          170
                   ....*....|
1U3S_A         199 LMLLSHVRHA 208
Cdd:smart00430 154 LLILPELRKI 163
Hormone_recep pfam00104
Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in ...
 23-209 3.91e-23

Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in binding the hormone in these receptors.


Pssm-ID: 459675 [Multi-domain]  Cd Length: 194  Bit Score: 92.41  E-value: 3.91e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A         23 SRPSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVL 102
Cdd:pfam00104   1 KSPPLKKLRKATKEELCELWERDLLLVAEWAKHFPEFQELPLEDQMALLKSFWLEWLRLEKAARSAKLRRKKILGEDVLM 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A        103 DRDEG--KCVEGILEIFDMLLATTSR----------------FRELKLQHKEYLCVKAMILLNssmyplvtatqdaDSSR 164
Cdd:pfam00104  81 ISDDDamKFVEDDSSWCTNYDLEQLLfflpffnsyffelvkpLRELNPDDEELAYLLAQLLFD-------------YAGD 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
1U3S_A        165 KLAHLLNAVTDALVWVIAKS--GISSQQQSMRLANLLMLLSHVRHAS 209
Cdd:pfam00104 148 GLSGEILEIVEKLQEKLANElhDYYVNKYSGRLAKLLKILPSLRKIS 194
 
Name Accession Description Interval E-value
NR_LBD_ER cd06949
Ligand binding domain of Estrogen receptor, which are activated by the hormone ...
 3-238 4.92e-130

Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen); The ligand binding domain (LBD) of Estrogen receptor (ER): Estrogen receptor, a member of nuclear receptor superfamily, is activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The C-terminal LBD also contains AF-2 activation motif, the dimerization motif, and part of the nuclear localization region. Estrogen receptor has been linked to aging, cancer, obesity and other diseases.


Pssm-ID: 132747  Cd Length: 235  Bit Score: 366.75  E-value: 4.92e-130
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A        3 LSPEQLVLTLLEAEPPHVLISR-PSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMM 81
Cdd:cd06949   1 LSAEQLISALLEAEPPHIYSEYdPTRPFTEASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLML 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       82 GLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVtaTQDAD 161
Cdd:cd06949  81 GLVWRSMEHPGKLLFAPDLLLDRNQGSCVEGMVEIFDMLLATASRFRELQLQREEYVCLKAIILLNSSVYTFL--LESLE 158

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
1U3S_A      162 SSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAH 238
Cdd:cd06949 159 SRRQVQRLLDKITDALVHACSKRGLSLQQQSRRLAQLLLILSHIRHVSNKGMEHLYSMKCKNVVPLYDLLLEMLDAH 235
NR_LBD_ER_like cd07068
The ligand binding domain of estrogen receptor and estrogen receptor-related receptors; The ...
 8-237 1.52e-107

The ligand binding domain of estrogen receptor and estrogen receptor-related receptors; The ligand binding domain of estrogen receptor (ER) and estrogen receptor-related receptors (ERRs): Estrogen receptors are a group of receptors which are activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. ERRs are closely related to the estrogen receptor (ER) family. But, it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signaling pathway, positively or negatively. ERRs share target genes, co-regulators and promoters with the estrogen receptor (ER) family. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER and ERRs have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132753  Cd Length: 221  Bit Score: 309.15  E-value: 1.52e-107
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A        8 LVLTLLEAEPPHVLISR-PSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWR 86
Cdd:cd07068   1 LLSALLVAEPDKLYAMNdPTGPDTEVSLLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWR 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       87 SIDHPGKLIFAPDLVLDRDEGKcVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLvtatqdaDSSRKL 166
Cdd:cd07068  81 SLPHPGKLVFAPDLLLDREQAR-VEGLLEIFDMLLQLVRRFRELGLQREEYVCLKAIILANSDVRHL-------EDREAV 152

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
1U3S_A      167 AHLLNAVTDALVWVIAKSGISsqQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNA 237
Cdd:cd07068 153 QQLRDAILDALVDVEAKRHGS--QQPRRLAQLLLLLPHLRQASNKGVRHLYSVKCEGKVPMYKLFLEMLEA 221
NR_LBD_ERR cd06946
The ligand binding domain of estrogen receptor-related nuclear receptors; The ligand binding ...
 8-237 9.29e-44

The ligand binding domain of estrogen receptor-related nuclear receptors; The ligand binding domain of estrogen receptor-related receptors (ERRs): The family of estrogen receptor-related receptors (ERRs), a subfamily of nuclear receptors, is closely related to the estrogen receptor (ER) family, but it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signaling pathway, positively or negatively. ERRs share target genes, co-regulators and promoters with the estrogen receptor (ER) family. There are three subtypes of ERRs: alpha, beta and gamma. ERRs bind at least two types of DNA sequence, the estrogen response element and another site, originally characterized as SF-1 (steroidogenic factor 1) response element. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ERR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132744  Cd Length: 221  Bit Score: 146.74  E-value: 9.29e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A        8 LVLTLLEAEPPHVLISR-PSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWR 86
Cdd:cd06946   1 ILSHLLVAEPDKLFAMPdPALPDSDIKALTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFR 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       87 SIDHPGKLIFAPDLVLDRDEGKCVeGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSmyplVTATQDADSSRKL 166
Cdd:cd06946  81 SLPFNGELVFAEDFILDEELAREA-GLLELYSACLQLVRRLQRLRLEKEEYVLLKALALANSD----SVHIEDVEAVRQL 155

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
1U3S_A      167 AH-LLNAVTDALvwviakSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNA 237
Cdd:cd06946 156 RDaLLEALSDYE------AGRHPGEAPRRAGQLLLTLPLLRQTDGKARRFFYGVKREGKVPMHKLFLEMLEA 221
NR_LBD_F2 cd06930
Ligand-binding domain of nuclear receptor family 2; Ligand-binding domain (LBD) of nuclear ...
 37-207 2.56e-32

Ligand-binding domain of nuclear receptor family 2; Ligand-binding domain (LBD) of nuclear receptor (NR) family 2: This is one of the major subfamily of nuclear receptors, including some well known nuclear receptors such as glucocorticoid receptor (GR), mineralocorticoid receptor (MR), estrogen receptor (ER), progesterone receptor (PR), and androgen receptor (AR), other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132728 [Multi-domain]  Cd Length: 165  Bit Score: 115.79  E-value: 2.56e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       37 SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHP--GKLIFAPDLVLDRDEGKCvEGIL 114
Cdd:cd06930   3 SLCELADRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFElsELLLPSPLLVILTEREAL-LGLA 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A      115 EIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLvtatqdaDSSRKLAHLLNAVTDALVWVIAKsgiSSQQQSMR 194
Cdd:cd06930  82 ELVQRLQELLSKLRSLQLDPKEYACLKAIVLFNPDLPGL-------KNQQQVEELQEKAQQALQEYIRK---RYPQQPAR 151

                       170
                ....*....|...
1U3S_A      195 LANLLMLLSHVRH 207
Cdd:cd06930 152 FAKLLLRLPELRS 164
NR_LBD cd06157
The ligand binding domain of nuclear receptors, a family of ligand-activated transcription ...
 38-206 1.42e-26

The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR): Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132726  Cd Length: 168  Bit Score: 100.84  E-value: 1.42e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       38 LTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVL---DRDEGKCVEGIL 114
Cdd:cd06157   3 LCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHtddDKEDEMKLLLKG 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A      115 EIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSmyplvtATQDADSSRKLAHLLNAVTDAL-VWVIAKSGissQQQSM 193
Cdd:cd06157  83 ELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPD------RKESLEDRKIVEELQERLLEALqDYLRKNYP---EEAPS 153

                       170
                ....*....|...
1U3S_A      194 RLANLLMLLSHVR 206
Cdd:cd06157 154 RFAKLLLLLPSLR 166
HOLI smart00430
Ligand binding domain of hormone receptors;
42-208 2.36e-26

Ligand binding domain of hormone receptors;


Pssm-ID: 214658  Cd Length: 163  Bit Score: 100.13  E-value: 2.36e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A          42 ADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGIL---EIFD 118
Cdd:smart00430   1 AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAPDGTYIRPDAVLELRKLfspFLDR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A         119 MLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQdadssRKLAHLLNAVTDALVWVIAKSGisSQQQSMRLANL 198
Cdd:smart00430  81 ILSELVKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGK-----EIVEKLQEKYANALHDYYLKNY--PMNYPGRFAKL 153

                          170
                   ....*....|
1U3S_A         199 LMLLSHVRHA 208
Cdd:smart00430 154 LLILPELRKI 163
NR_LBD_RXR_like cd06943
The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear ...
 42-216 6.08e-24

The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily; The ligand binding domain of the retinoid X receptor (RXR) and Ultraspiracle (USP): This family includes two evolutionary related nuclear receptors: retinoid X receptor (RXR) and Ultraspiracle (USP). RXR is a nuclear receptor in mammalian and USP is its counterpart in invertebrates. The native ligand of retinoid X receptor is 9-cis retinoic acid (RA). RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. RXRs can play different roles in these heterodimers. It acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear receptors. Ultraspiracle (USP) plays similar roles as DNA binding partner of other nuclear rec eptors in invertebrates. USP has no known high-affinity ligand and is thought to be a silent component in the heterodimeric complex with partner receptors. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, RXR and USP have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132741  Cd Length: 207  Bit Score: 95.05  E-value: 6.08e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       42 ADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVeGILEIFDMLL 121
Cdd:cd06943  39 ADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSIAVKDGILLATGLHLHRNSAHQA-GVGAIFDRIL 117

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A      122 AT-TSRFRELKLQHKEYLCVKAMILLNssmyPLVTATQDADSSRKLAHLLNAVTDALVwviaKSGISSQQQsmRLANLLM 200
Cdd:cd06943 118 TElVVKMRDLKMDRTELGCLRAIILFN----PDVKGLKSRQEVESLREKVYASLEEYC----RQKHPEQPG--RFAKLLL 187

                       170
                ....*....|....*.
1U3S_A      201 LLSHVRHASNKGMEHL 216
Cdd:cd06943 188 RLPALRSIGLKCLEHL 203
Hormone_recep pfam00104
Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in ...
 23-209 3.91e-23

Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in binding the hormone in these receptors.


Pssm-ID: 459675 [Multi-domain]  Cd Length: 194  Bit Score: 92.41  E-value: 3.91e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A         23 SRPSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVL 102
Cdd:pfam00104   1 KSPPLKKLRKATKEELCELWERDLLLVAEWAKHFPEFQELPLEDQMALLKSFWLEWLRLEKAARSAKLRRKKILGEDVLM 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A        103 DRDEG--KCVEGILEIFDMLLATTSR----------------FRELKLQHKEYLCVKAMILLNssmyplvtatqdaDSSR 164
Cdd:pfam00104  81 ISDDDamKFVEDDSSWCTNYDLEQLLfflpffnsyffelvkpLRELNPDDEELAYLLAQLLFD-------------YAGD 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
1U3S_A        165 KLAHLLNAVTDALVWVIAKS--GISSQQQSMRLANLLMLLSHVRHAS 209
Cdd:pfam00104 148 GLSGEILEIVEKLQEKLANElhDYYVNKYSGRLAKLLKILPSLRKIS 194
NR_LBD_GR_Like cd06947
Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid ...
 9-148 2.47e-22

Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid receptor , progesterone receptor, and androgen receptor; The ligand binding domain of GR_like nuclear receptors: This family of NRs includes four distinct, but closely related nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). These four receptors play key roles in some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family use multiple signaling pathways and share similar functional mechanisms. The dominant signaling pathway is via direct DNA binding and transcriptional regulation of target genes. Another mechanism is via protein-protein interactions, mainly with other transcription factors such as nuclear factor-kappaB and activator protein-1, to regulate gene expression patterns. Both pathways can up-regulate or down-regulate gene expression and require ligand activation of the receptor and recruitment of other cofactors such as chaperone proteins and coregulator proteins. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GR, MR, PR, and AR share the same modular structure with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132745  Cd Length: 246  Bit Score: 91.65  E-value: 2.47e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A        9 VLTLLEAEPPHVLIS--RPSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWR 86
Cdd:cd06947   2 LLSVLEAIEPEVVYAgyDNSQPDTTARLLSSLNRLGERQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWR 81

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....
1U3S_A       87 SIDH--PGKLIFAPDLVLDRDEGKcVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNS 148
Cdd:cd06947  82 SYKHvnSQMLYFAPDLVFNEQRMH-QSAMYSLCLGMRQISQEFVRLQVTYEEFLCMKVLLLLST 144
NR_LBD_Nurr1_like cd06945
The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear ...
 41-227 7.00e-22

The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear receptor superfamily; The ligand binding domain of nuclear receptor Nurr1_like: This family of nuclear receptors, including Nurr1, Nerve growth factor-induced-B (NGFI-B) and DHR38 are involved in the embryo development. Nurr1 is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of tr anscriptional initiation. Another group of receptor in this family is DHR38. DHR38 is the Drosophila homolog to the vertebrate NGFI-B-type orphan receptor. It interacts with the USP component of the ecdysone receptor complex, suggesting that DHR38 might modulate ecdysone-triggered signals in the fly, in addition to the ECR/USP pathway. Nurr1_like proteins exhibit a modular structure that is characteristic for nuclear receptors; they have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132743 [Multi-domain]  Cd Length: 239  Bit Score: 90.15  E-value: 7.00e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       41 LADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEgkCVEGILEIFDML 120
Cdd:cd06945  49 LLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDGKLVFCNGLVLHRLQ--CVRGFGEWLDSI 126

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A      121 LATTSRFRELKLQHKEYLCVKAMILlnssmypLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSmRLANLLM 200
Cdd:cd06945 127 LAFSSSLQSLLLDDISAFCCLALLL-------LITERHGLKEPKKVEELQNKIISCLRDHVTSNYPGQDKPN-RLSKLLL 198

                       170       180
                ....*....|....*....|....*..
1U3S_A      201 LLSHVRHASNKGMEHLLNMKCKNVVPV 227
Cdd:cd06945 199 KLPELRTLSKKGLQRIFFLKLEDLLPP 225
NR_LBD_PR cd07074
Ligand binding domain of the progesterone receptor, a member of the nuclear hormone receptor; ...
 9-148 3.78e-21

Ligand binding domain of the progesterone receptor, a member of the nuclear hormone receptor; The ligand binding domain of the progesterone receptor (PR): PR is a member of the nuclear receptor superfamily of ligand dependent transcription factors, mediating the biological actions of progesterone. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, protein processing, and metabolism. When no binding hormone is present the carboxyl terminal inhibits transcription. Binding to a hormone induces a structural change that removes the inhibitory action. After progesterone binds to the receptor, PR forms a dimer and the complex enters the nucleus where it interacts with the hormone response element (HRE) in the promoters of progesterone responsive genes and alters their transcription. In addition, rapid actions of PR that occur independent of transcription, have also been observed in several tissues like brain, liver, mammary gland and spermatozoa. There are two natural PR isoforms called PR-A and PR-B. PR-B has an additional stretc h of 164 amino acids at the N terminus. The extra domain in PR-B performs activation functions by recruiting coactivators that could not be recruited by PR-A. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The LBD is not only involved in binding to progesterone, but also involved in coactivator binding and dimerization.


Pssm-ID: 132759  Cd Length: 248  Bit Score: 88.46  E-value: 3.78e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A        9 VLTLLEAEPPHVLIS--RPSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWR 86
Cdd:cd07074   2 LINLLMSIEPDVVYAgyDNTKPETPSSLLTSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWR 81

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
1U3S_A       87 SIDH--PGKLIFAPDLVLDRDEGKCVegilEIFDMLLAT---TSRFRELKLQHKEYLCVKAMILLNS 148
Cdd:cd07074  82 SYKHvsGQMLYFAPDLILNEQRMKES----SFYSLCLTMwqiPQEFVKLQVSQEEFLCMKALLLLNT 144
NR_LBD_GR cd07076
Ligand binding domain of the glucocorticoid receptor, a member of the nuclear receptor ...
 9-148 1.16e-19

Ligand binding domain of the glucocorticoid receptor, a member of the nuclear receptor superfamily; The ligand binding domain of the glucocorticoid receptor (GR): GR is a ligand-activated transcription factor belonging to the nuclear receptor superfamily. It binds with high affinity to cortisol and other glucocorticoids. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. In the absence of hormone, the glucocorticoid receptor (GR) is complexes with a variety of heat shock proteins in the cytosol. The binding of the glucocorticoids results in release of the heat shock proteins and transforms it to its active state. One mechanism of action of GR is by direct activation of gene transcription. The activated form of GR forms dimers, translocates into the nucleus, and binds to specific hormone responsive elements, activating gene transcription. GR can also function as a repressor of other gene transcription activators, such as NF-kappaB and AF-1 by directly binding to them, and bloc king the expression of their activated genes. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The LBD also functions for dimerization and chaperone protein association.


Pssm-ID: 132761  Cd Length: 247  Bit Score: 84.60  E-value: 1.16e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A        9 VLTLLEAEPPHVLIS--RPSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWR 86
Cdd:cd07076   2 LVSLLEVIEPEVLYSgyDSSVPDSTWRIMSTLNMLGGRQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWR 81

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....
1U3S_A       87 SIDHPGK--LIFAPDLVLDRDEGKcVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNS 148
Cdd:cd07076  82 SYRQSNGnlLCFAPDLIINEQRMT-LPCMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLST 144
NR_LBD_MR cd07075
Ligand binding domain of the mineralocorticoid receptor, a member of the nuclear receptor ...
 26-148 3.66e-18

Ligand binding domain of the mineralocorticoid receptor, a member of the nuclear receptor superfamily; The ligand binding domain of the mineralocorticoid receptor (MR): MR, also called aldosterone receptor, is a member of nuclear receptor superfamily involved in the regulation of electrolyte and fluid balance. The receptor is activated by mineralocorticoids such as aldosterone and deoxycorticosterone as well as glucocorticoids, like cortisol and cortisone. Binding of its ligand results in its translocation to the cell nucleus, homodimerization and binding to hormone response elements (HREs) present in the promoter of MR controlled genes. This results in the recruitment of the coactivators and the transcription of the activated genes. MR is expressed in many tissues and its activation results in the expression of proteins regulating electrolyte and fluid balance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, MR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD ). The LBD, in addition to binding ligand, contains a ligand-dependent activation function-2 (AF-2).


Pssm-ID: 132760  Cd Length: 248  Bit Score: 80.75  E-value: 3.66e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       26 SAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGK--LIFAPDLVLD 103
Cdd:cd07075  21 SKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRSYKHTNSqfLYFAPDLVFN 100

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
1U3S_A      104 RDEGKcVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNS 148
Cdd:cd07075 101 EERMH-QSAMYELCQGMHQISLQFVRLQLTFEEYTIMKVLLLLST 144
NR_LBD_DHR4_like cd06953
The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4; The ...
 12-214 6.18e-18

The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4; The ligand binding domain of Ecdysone-induced receptor DHR4: Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132751  Cd Length: 213  Bit Score: 79.34  E-value: 6.18e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       12 LLEAEPPHVLIS----RPSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWR- 86
Cdd:cd06953   2 LLVAEDLEPLITpmliEDGATVDQAELFALLCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITVa 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       87 SIDHPGKLIFAPDLVLDRDEG--KCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSR 164
Cdd:cd06953  82 SLQNLGLLQDCLSKYLPSEDEleRFGDEGGEVVERLTYLLAKFRQLKVSNEEYVCLKVINFLNQDIDGLTNASQLESLQK 161

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|
1U3S_A      165 KLAHLLNAVTDAlvwviaksgiSSQQQSMRLANLLMLLSHVRHASNKGME 214
Cdd:cd06953 162 RYWYVLQDFTEL----------NYPNQPNRFSDLLSCLPEIRAAAGKLLH 201
NR_LBD_NGFI-B cd07348
The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors; The ...
 52-226 2.01e-16

The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors; The ligand binding domain of Nerve growth factor-induced-B (NGFI-B): NGFI-B is a member of the nuclear#steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of the embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcriptional initiation. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, NGFI-B has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132762  Cd Length: 238  Bit Score: 75.63  E-value: 2.01e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       52 WAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEgkCVEGILEIFDMLLATTSRFRELK 131
Cdd:cd07348  60 WAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEGKLIFCNGVVLHRTQ--CVRGFGDWIDSILEFSQSLHRMN 137

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A      132 LQHKEYLCVKAMIllnssmypLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGiSSQQQSMRLANLLMLLSHVRHASNK 211
Cdd:cd07348 138 LDVSAFSCLAALV--------IITDRHGLKEPKRVEELQNRLISCLKEHVSGSA-SEPQRPNCLSRLLGKLPELRTLCTQ 208

                       170
                ....*....|....*
1U3S_A      212 GMEHLLNMKCKNVVP 226
Cdd:cd07348 209 GLQRIFYLKLEDLVP 223
NR_LBD_AR cd07073
Ligand binding domain of the nuclear receptor androgen receptor, ligand activated ...
 8-147 5.88e-16

Ligand binding domain of the nuclear receptor androgen receptor, ligand activated transcription regulator; The ligand binding domain of the androgen receptor (AR): AR is a member of the nuclear receptor family. It is activated by binding either of the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for male primary sexual characteristics and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of an androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR-regulated genes and modulates their expression. Another mode of action is independent of their interactions with DNA. The receptors interact directly with signal transduction proteins in the cytoplasm, causing rapid changes in cell function, such as ion transport. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, AR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The LBD is not only involved in binding to androgen, but also involved in binding of coactivator proteins and dimerization. A ligand dependent nuclear export signal is also present at the ligand binding domain.


Pssm-ID: 132758  Cd Length: 246  Bit Score: 74.59  E-value: 5.88e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A        8 LVLTLLEAEPPHVLIS--RPSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMW 85
Cdd:cd07073   1 IFLNVLEAIEPGVVCAghDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGW 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
1U3S_A       86 RSIDHPGK--LIFAPDLVLD-------RDEGKCVEgileifdmLLATTSRFRELKLQHKEYLCVKAMILLN 147
Cdd:cd07073  81 RSFTNVNSrmLYFAPDLVFNeyrmhksRMYSQCVR--------MRHLSQEFGWLQITPQEFLCMKALLLFS 143
NR_LBD_Ftz-F1_like cd06944
The ligand binding domain of FTZ-F1 like nuclear receptors; The ligand binding domain of ...
 40-237 7.34e-16

The ligand binding domain of FTZ-F1 like nuclear receptors; The ligand binding domain of FTZ-F1 like nuclear receptors: This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which required at several stages of development. Particularly, FTZ-F1 genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. SF-1 is an essential regulator of endocrine development and function and is considered a master regulator of reproduction; SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). However, the ligand for FTZ-F1 has not yet been identified. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 and SF-1 bind to DNA as a monomer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, receptors in this family have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132742 [Multi-domain]  Cd Length: 237  Bit Score: 73.85  E-value: 7.34e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       40 KLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDH--PGKLIFAPDLVLDRDEGKCVEGILeIF 117
Cdd:cd06944  45 KMADQTLFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHgkEDSILLVTGQEVDLSTLASQAGLG-LS 123

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A      118 DMLLATT---SRFRELKLQHKEYLCVKAMILLNSSM-----YPLVTATQDADSSRKLAHLLNAVTdalvwviaksgissq 189
Cdd:cd06944 124 SLVDRAQelvNKLRELQFDRQEFVCLKFLILFNPDVkglenRQLVESVQEQVNAALLDYTLCNYP--------------- 188

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*...
1U3S_A      190 QQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNA 237
Cdd:cd06944 189 QQTDKFGQLLLRLPEIRAISMQAEEYLYYKHLNGEVPCNNLLIEMLHA 236
NR_LBD_Lrh-1 cd07069
The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor ...
 38-237 1.97e-15

The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,; The ligand binding domain (LBD) of the liver receptor homolog-1 (LRH-1): LRH-1 belongs to nuclear hormone receptor superfamily, and is expressed mainly in the liver, intestine, exocrine pancreas, and ovary. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 binds DNA as a monomer, and is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. Recently, phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, LRH-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132754 [Multi-domain]  Cd Length: 241  Bit Score: 73.14  E-value: 1.97e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       38 LTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDH--PGKLIFAPDLVLD-----RDEGKCV 110
Cdd:cd07069  45 MCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHgkEGSIFLVTGQQVDysiiaSQAGATL 124

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A      111 EGILEIFDMLLAttsRFRELKLQHKEYLCVKAMILLNSSM-----YPLVTATQDADSSRKLAHLLnavtdalvwviaksg 185
Cdd:cd07069 125 NNLMSHAQELVA---KLRSLQFDQREFVCLKFLVLFSLDVknlenFQLVEGVQEQVNAALLDYTM--------------- 186

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|..
1U3S_A      186 ISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNA 237
Cdd:cd07069 187 CNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHA 238
NR_LBD_Nurr1 cd07071
The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors; The ...
 52-226 6.44e-15

The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors; The ligand binding domain of nuclear receptor Nurr1: Nurr1 belongs to the conserved family of nuclear receptors. It is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Nurr1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132756  Cd Length: 238  Bit Score: 71.60  E-value: 6.44e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       52 WAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEgkCVEGILEIFDMLLATTSRFRELK 131
Cdd:cd07071  60 WAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQ--CVRGFGEWIDSIVEFSSNLQNMN 137

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A      132 LQHKEYLCVKAMillnssmyPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSmRLANLLMLLSHVRHASNK 211
Cdd:cd07071 138 IDISAFSCIAAL--------AMVTERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPN-YLSKLLGKLPELRTLCTQ 208

                       170
                ....*....|....*
1U3S_A      212 GMEHLLNMKCKNVVP 226
Cdd:cd07071 209 GLQRIFYLKLEDLVP 223
NR_LBD_HNF4_like cd06931
The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in ...
 9-234 2.08e-14

The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes; The ligand binding domain of hepatocyte nuclear factor 4 (HNF4) like proteins: HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is constitutively active as a transcription activator. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, HNF4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The LBD domain is also responsible for recruiting co-activator proteins. More than 280 nuclear receptors are found in C. ele gans, most of which are originated from an explosive burst of duplications of HNF4.


Pssm-ID: 132729  Cd Length: 222  Bit Score: 69.71  E-value: 2.08e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A        9 VLTLLEAEPPHVLISRPSAPFTEASMMMSLTKLAD------KELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMG 82
Cdd:cd06931   2 ISVLLQAEALSRQQSSPIPTCSGDIRPKKIASINDvcesmkQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLG 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       83 LMWRSIDHPGKLIFAPDLVLDRD--EGKCVEGILEIFDMLLATtsrFRELKLQHKEYLCVKAMILLNssmyPLVTATQDA 160
Cdd:cd06931  82 VARRSMPYKDILLLGNDLIIPRHcpEPEISRVANRILDELVLP---LRDLNIDDNEYACLKAIVFFD----PDAKGLSDP 154

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
1U3S_A      161 DSSRKLAH-LLNAVTDAlvwviaksgISSQQ--QSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEM 234
Cdd:cd06931 155 QKIKRLRFqVQVSLEDY---------INDRQydSRGRFGELLLLLPTLQSITWQMIEQIQFARLFGVAKIDNLLQEM 222
NR_LBD_SF-1 cd07070
The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear ...
 7-237 6.24e-12

The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear receptor superfamily; The ligand binding domain of nuclear receptor steroidogenic factor 1 (SF-1): SF-1, a member of the nuclear hormone receptor superfamily, is an essential regulator of endocrine development and function and is considered a master regulator of reproduction. Most nuclear receptors function as homodimer or heterodimers, however SF-1 binds to its target genes as a monomer, recognizing the variations of the DNA sequence motif, T/CCA AGGTCA. SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been determined as potential ligands of SF-1. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, SF-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132755  Cd Length: 237  Bit Score: 63.05  E-value: 6.24e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A        7 QLVLTLLEAEPPHVLI-------------SRPSAPfteaSMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLES 73
Cdd:cd07070   3 ELILQLLQLEPDEDQVrarilgclqepqkSRPDQP----APFGLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQN 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       74 CWMEVLMMGLMWRSIDH--PGKLIFAPDLVLDRDEGKCVEG------ILEIFDMLLATTSrfreLKLQHKEYLCVKAMIL 145
Cdd:cd07070  79 CWSELLVFDHIYRQVQHgkEGSILLVTGQEVELSTVAAQAGsllhslVLRAQELVLQLHA----LQLDRQEFVCLKFLIL 154

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A      146 LNSSMYPLVTATQDADSSRKLAhllNAVTDALVWVIAKSGISSQQqsmrlanLLMLLSHVRHASNKGMEHLLNMKCKNVV 225
Cdd:cd07070 155 FSLDVKFLNNHSLVKDAQEKAN---AALLDYTLCHYPHCGDKFQQ-------LLLRLVEVRALSMQAKEYLYHKHLGNEM 224

                       250
                ....*....|..
1U3S_A      226 PVYDLLLEMLNA 237
Cdd:cd07070 225 PRNNLLIEMLQA 236
NR_LBD_Tlx_PNR_like cd06950
The ligand binding domain of Tailless-like proteins, orphan nuclear receptors; The ligand ...
 50-220 1.70e-11

The ligand binding domain of Tailless-like proteins, orphan nuclear receptors; The ligand binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like family: This family includes photoreceptor cell-specific nuclear receptor (PNR), Tailless (TLX), and related receptors. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX and PNR have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132748 [Multi-domain]  Cd Length: 206  Bit Score: 61.54  E-value: 1.70e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       50 ISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIfDMLLATTSRFRE 129
Cdd:cd06950  43 VKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLPLDSCPLLAVPGLSPDNTEAERTFLSEV-RALQETLSRFRQ 121

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A      130 LKLQHKEYLCVKAMILLNSSMYPL-----VTATQDAdssrklAHL-LNavtdalvwviakSGISSQQ--QSMRLANLLML 201
Cdd:cd06950 122 LRVDATEFACLKAIVLFKPETRGLkdpaqVEALQDQ------AQLmLN------------KHIRTRYptQPARFGKLLLL 183

                       170
                ....*....|....*....
1U3S_A      202 LSHVRHASNKGMEHLLNMK 220
Cdd:cd06950 184 LPSLRFISSSTIEELFFKK 202
NR_LBD_F1 cd06929
Ligand-binding domain of nuclear receptor family 1; Ligand-binding domain (LBD) of nuclear ...
 33-216 2.47e-09

Ligand-binding domain of nuclear receptor family 1; Ligand-binding domain (LBD) of nuclear receptor (NR) family 1: This is one of the major subfamily of nuclear receptors, including thyroid receptor, retinoid acid receptor, ecdysone receptor, farnesoid X receptor, vitamin D receptor, and other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132727  Cd Length: 174  Bit Score: 54.92  E-value: 2.47e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       33 SMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWR------SIDHPGKLIFAPDLVLDRDE 106
Cdd:cd06929   2 EKFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLydpeknSLTFGDGKGNSRDVLLNGGF 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A      107 GKCVEGILEIFDmllattsRFRELKLQHKEYLCVKAMILLNssmyPLVTATQDADSSRKL-AHLLNAVtDALVwviaksG 185
Cdd:cd06929  82 GEFIEPLFEFAE-------KMNKLQLDDNEYALLTAIVLFS----PDRPGLQDVDTVEKLqERLLEAL-QRYL------K 143

                       170       180       190
                ....*....|....*....|....*....|.
1U3S_A      186 ISSQQQSMRLANLLMLLSHVRHASNKGMEHL 216
Cdd:cd06929 144 VNHPDAPQMFAKLLKKLTELRTLNELHAELL 174
NR_LBD_RAR cd06937
The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear ...
 25-235 4.02e-08

The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily; The ligand binding domain (LBD) of retinoic acid receptor (RAR): Retinoic acid receptors are members of the nuclear receptor (NR) superfamily of ligand-regulated transcription factors. RARs mediate the biological effect of retinoids, including both naturally dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RARs function as heterodimers with retinoic X receptors by binding to specific RAR response elements (RAREs) found in the promoter regions of retinoid target genes. In the absence of ligand, the RAR-RXR heterodimer recruits the corepressor proteins NCoR or AMRT, and associated factors such as histone deacetylases or DNA-methyltransferases, leading to an inactive condensed chromatin structure, preventing transcription. Upon ligand binding, the corepressors are released, and coactivator complexes such as histone acetyltransferase or histone arginine methyltransferases are recruited to activate transcription. There are three RAR subtypes (alpha, beta, gamma), originating from three distinct genes. For each subtype, several isoforms exist that differ in their N-terminal region, allowing retinoids to exert their pleiotropic effects. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoic acid receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132735  Cd Length: 231  Bit Score: 52.12  E-value: 4.02e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       25 PSAPFTEASMMMSL----TKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDL 100
Cdd:cd06937  26 NSSADQRVRLDLGLwdkfSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGL 105

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A      101 VLDRDEGKcVEGILEIFDMLLATTSRFRELKLQHKEylcvkamILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWV 180
Cdd:cd06937 106 TLNRTQMH-NAGFGPLTDLVFTFANQLLPLEMDDTE-------IGLLSAICLICGDRQDLEEPDRVEKLQEPLLEALKIY 177

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*
1U3S_A      181 IAKSGISSQQqsmRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEML 235
Cdd:cd06937 178 ARKRRPDKPH---MFPKMLMKITDLRSISAKGAERVITLKMEIPGPMPPLISEML 229
NR_LBD_DHR38_like cd07072
Ligand binding domain of DHR38_like proteins, members of the nuclear receptor superfamily; ...
 28-234 1.59e-07

Ligand binding domain of DHR38_like proteins, members of the nuclear receptor superfamily; The ligand binding domain of nuclear receptor DHR38_like proteins: DHR38 is a member of the steroid receptor superfamily in Drosophila. DHR38 interacts with the USP component of the ecdysone receptor complex, suggesting that DHR38 might modulate ecdysone-triggered signals in the fly, in addition to the ECR/USP pathway. At least four differentially expressed mRNA isoforms have been detected during development. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR38 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132757  Cd Length: 239  Bit Score: 50.59  E-value: 1.59e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       28 PFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEg 107
Cdd:cd07072  37 PMSEAEKVQQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPEDTKLTFCNGVVLHKQQ- 115

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A      108 kCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMIllnssmypLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGiS 187
Cdd:cd07072 116 -CQRSFGDWLHAILEFSKSLHAMDIDISAFACLCALT--------LITERHGLKEPHKVEQLQMKIISSLRDHVTYNA-E 185

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
1U3S_A      188 SQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEM 234
Cdd:cd07072 186 AQKKPHYFSRLLGKLPELRSLSVQGLQRIFYLKLEDLVPAPPLIENM 232
NR_LBD_LXR cd06954
The ligand binding domain of Liver X receptors, a family of nuclear receptors of ...
 27-223 2.64e-07

The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors; The ligand binding domain of Liver X receptors: Liver X receptors (LXRs) belong to a family of nuclear receptors of ligand-activated transcription factors. LXRs operate as cholesterol sensors which protect from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. Upon ligand binding a conformational change leads to recruitment of co-factors, which stimulates expression of target genes. Among the LXR target genes are several genes involved in cholesterol efflux from peripheral tissues such as the ATP-binding-cassette transporters ABCA1, ABCG1 and ApoE. There are two LXR isoforms in mammals, LXRalpha and LXRbeta. LXRalpha is expressed mainly in the liver, intestine, kidney, spleen, and adipose tissue, whereas LXRbeta is ubiquitously expressed at lower level. Both LXRalpha and LXRbeta function as heterodimers with the retinoid X receptor (RX R) which may be activated by either LXR ligands or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. LXR has typical NR modular structure with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and the ligand binding domain (LBD) at the C-terminal.


Pssm-ID: 132752  Cd Length: 236  Bit Score: 49.75  E-value: 2.64e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       27 APFTEasmmmsLTKLADKELVhmiSWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMwRSIDHPGKLI-FAPDLVLDRD 105
Cdd:cd06954  46 AHFTE------LAILSVQEIV---DFAKQLPGFLTLTREDQIALLKASTIEVMLLETA-RRYNPESEAItFLKDFPYSRD 115

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A      106 EGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLnSSMYPLVtatQDADSSRKLAHllnAVTDALVWVIAksg 185
Cdd:cd06954 116 DFARAGLQVEFINPIFEFSKSMRELQLDDAEYALLIAINIF-SADRPNV---QDHHRVERLQE---TYVEALHSYIK--- 185

                       170       180       190
                ....*....|....*....|....*....|....*...
1U3S_A      186 ISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKN 223
Cdd:cd06954 186 IKRPSDRLMFPRMLMKLVSLRTLSSVHSEQVFALRLQD 223
NR_LBD_COUP-TF cd06948
Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member ...
 37-235 4.75e-07

Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member of the nuclear receptor family; The ligand binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs): COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. In mammals two isoforms named COUP-TFI and COUP-TFII have been identified. Both genes show an exceptional homology and overlapping expression patterns, suggesting that they may serve redundant functions. Although COUP-TF was originally characterized as a transcriptional activator of the chicken ovalbumin gene, COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone receptors, such as retinoic acid receptor (RAR), thyroid hormone receptor (TR), vitamin D receptor (VDR), peroxisome proliferator activated receptor (PPAR), and hepatocyte nuclear factor 4 (HNF4). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, COUP-TFs have a central well cons erved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132746  Cd Length: 236  Bit Score: 48.99  E-value: 4.75e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       37 SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGlmwrSIDHPGKLIFAPDLV--------LDRDEGK 108
Cdd:cd06948  34 NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLN----AAQCCMPLHVAPLLAaaglhaspMSADRVV 109

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A      109 CVEGILEIFDMLLattSRFRELKLQHKEYLCVKAMILLNSsmyplvtatqDADSSRKLAHLLNAVTDALVWVIAKSGISS 188
Cdd:cd06948 110 AFMDHIRIFQEQV---EKLKALHVDSAEFSCLKAIVLFTS----------DACGLSDPAHIESLQEKSQCALEEYVRTQY 176

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
1U3S_A      189 QQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEML 235
Cdd:cd06948 177 PNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDML 223
NR_LBD_SHP cd07349
The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain; The ...
 40-235 5.58e-05

The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain; The ligand binding domain of the Small Heterodimer Partner (SHP): SHP is a member of the nuclear receptor superfamily. SHP has a ligand binding domain, but lacks the DNA binding domain, typical to almost all of the nuclear receptors. It functions as a transcriptional coregulator by directly interacting with other nuclear receptors through its AF-2 motif. The closest relative of SHP is DAX1 and they can form heterodimer. SHP is an orphan receptor, lacking an identified ligand.


Pssm-ID: 132763  Cd Length: 222  Bit Score: 42.88  E-value: 5.58e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       40 KLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDL----VLDRDEGKCVEGILE 115
Cdd:cd07349  26 REASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVAEAPVPSMlkkiLLEGQSSSGGSGQPD 105

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A      116 IFDMLLATTSR-------FRELKLQHKEYLCVKAMILLNSSMyPLVTATQDADSSRKLAHllnavtDALVWVIakSGISS 188
Cdd:cd07349 106 RPQPSLAAVQWlqcclnkFWSLDLSPKEYAYLKGTILFNPDV-PGLTASSHVGHLQQEAQ------WALCEVL--EPLHP 176

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
1U3S_A      189 QQQSmRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEML 235
Cdd:cd07349 177 QDQG-RFARILLTASTLKSIPPSLITDLFFRPIIGDADIAELLGDML 222
NR_LBD_EcR cd06938
The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors ...
 49-223 1.13e-04

The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors super family; The ligand binding domain (LBD) of the ecdysone receptor: The ecdysone receptor (EcR) belongs to the superfamily of nuclear receptors (NRs) of ligand-dependent transcription factors. Ecdysone receptor is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. ECR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of ecdysone receptor are ecdysteroids#the endogenous steroidal hormones found in invertebrates. In addition, insecticide bisacylhydrazine used against pests has shown to act on EcR. EcR must be dimerised with a USP for high-affinity ligand binding to occur. The ligand binding triggers a conformational change in the C-terminal part of the EcR ligand-binding domain that leads to transcriptional activation of genes controlled by EcR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ec dysone receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132736 [Multi-domain]  Cd Length: 231  Bit Score: 42.04  E-value: 1.13e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       49 MISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKcVEGILEIFDMLLATTSRFR 128
Cdd:cd06938  55 IVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTDSIVFANNQPYTRDSYR-KAGMGDSAEDLFRFCRAMC 133

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A      129 ELKLQHKEYLCVKAMILLnSSMYPLVTAtqdadssRKLAHLLNAVTDAL-VWVIAKsgiSSQQQSMRLANLLMLLSHVRH 207
Cdd:cd06938 134 SMKVDNAEYALLTAIVIF-SDRPGLLQP-------KKVEKIQEIYLEALrAYVDNR---RPPSQRVIFAKLLSILTELRT 202

                       170
                ....*....|....*.
1U3S_A      208 ASNKGMEHLLNMKCKN 223
Cdd:cd06938 203 LGNQNSEMCFSLKLKN 218
NR_LBD_TR cd06935
The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear ...
 17-79 1.36e-04

The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear receptors; The ligand binding domain (LBD) of thyroid hormone receptors: Thyroid hormone receptors are members of a superfamily of nuclear receptors. Thyroid hormone receptors (TR) mediate the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the heart to regulate heart rate and rhythm and TRbeta is active in the liver and other tissues. The unliganded TRs function as transcription repressors, by binding to thyroid hormone response elements (TRE) predominantly as homodimers, or as heterodimers with retinoid X-receptors (RXR), and being associated with a complex of proteins containing corepressor proteins. Ligand binding promotes corepressor dissociation and binding of a coactivator to activate transcription. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132733  Cd Length: 243  Bit Score: 42.11  E-value: 1.36e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
1U3S_A       17 PPHVLISRPSAPFTEASMM-----MSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVL 79
Cdd:cd06935  31 LPEDIGQAPIVSAPDGDKVdleafSHFTKIITPAITRVVDFAKKLPMFTELPCEDQIILLKGCCMEIM 98
NR_LBD_ROR_like cd06939
The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor ...
 48-220 1.88e-04

The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily; The ligand binding domain (LBD) of Retinoid-related orphan receptors (RORs): Retinoid-related orphan receptors (RORs) are transcription factors belonging to the nuclear receptor superfamily. RORs are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. Transcription regulation by RORs is mediated through certain corepressors, as well as coactivators. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma that differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum, particularly in the regulation of the maturation and survival of Purkinje cells. RORbeta expression is largely restricted to several regions of the brain, the retina, and pineal gland. RORgamma is essential for lymph node organogenesis. Recently, it has been su ggested that cholesterol or a cholesterol derivative is the natural ligand of RORalpha. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoid-related orphan receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132737 [Multi-domain]  Cd Length: 241  Bit Score: 41.58  E-value: 1.88e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       48 HMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMgLMWRSIDHPGKLIFAPDLVLDRDEGK---CVEGILEIFDMLLATT 124
Cdd:cd06939  63 YVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLV-RMSRAFNPSNNTVLFDGKYAPIDLFKslgCDDLISAVFDFAKSLC 141

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A      125 srfrELKLQHKEYLCVKAMILLNSSMYPLvtatqdaDSSRKLAHLLNAVTDALVWVIAKsgisSQQQSMRLANLLMLLSH 204
Cdd:cd06939 142 ----ELKLTEDEIALFSALVLISADRPGL-------QEKRKVEKLQQKIELALRHVLQK----NHGDDTILTKLLAKMPT 206

                       170
                ....*....|....*.
1U3S_A      205 VRHASNKGMEHLLNMK 220
Cdd:cd06939 207 LRALCSLHMEKLQKFK 222
NR_LBD_Dax1_like cd06951
The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain; The ...
 46-147 4.15e-04

The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain; The ligand binding domain of DAX1-like proteins: This orphan nuclear receptor family includes DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) and the Small Heterodimer Partner (SHP). Both receptors have a typical ligand binding domain, but lack the DNA binding domain, typical to almost all of the nuclear receptors. They function as a transcriptional coregulator by directly interacting with other nuclear receptors. DAX1 and SHP can form heterodimers with each other, as well as with many other nuclear receptors. In addition, DAX1 can also form homodimers. DAX1 plays an important role in the normal development of several hormone-producing tissues. SHP has shown to regulate a variety of target genes.


Pssm-ID: 132749 [Multi-domain]  Cd Length: 222  Bit Score: 40.18  E-value: 4.15e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       46 LVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDL---VLDRDE---GKCVEGILEIFDM 119
Cdd:cd06951  32 LLKTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVPFDTVEVPAPSIlceILTGAEmhwGGTPPPTLTMPPC 111

                        90       100       110
                ....*....|....*....|....*....|....*.
1U3S_A      120 LLATT--------SRFRELKLQHKEYLCVKAMILLN 147
Cdd:cd06951 112 IPLADvqdiqqflMKCWSLDLDCKEYAYLKGAVLFT 147
NR_LBD_VDR cd06933
The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily; ...
 28-81 4.73e-04

The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily; The ligand binding domain of vitamin D receptors (VDR): VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of corepressors. Upon ligand binding, VDR forms heterodimer with the retinoid X receptor (RXR) that binds to vitamin D response elements (VDREs), recruits coactivators. This leads to the expression of a large number of genes. Approximately 200 human genes are considered to be primary targets of VDR and even more genes are regulated indirectly. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, VDR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132731  Cd Length: 238  Bit Score: 40.34  E-value: 4.73e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
1U3S_A       28 PFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMM 81
Cdd:cd06933  32 PPVRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEVIML 85
NR_LBD_REV_ERB cd06940
The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily; ...
 49-220 1.13e-03

The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily; The ligand binding domain (LBD) of REV-ERB receptors: REV-ERBs are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. The LBD domain of REV-ERB is unusual in the nuclear receptor family by lacking the AF-2 region that is responsible for coactivator interaction. REV-ERBs act as constitutive repressors because of their inability to bind coactivators. REV-ERB receptors can bind to two classes of DNA response elements as either a monomer or heterodimer, indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target gene. The porphyrin heme has been demonstrated to function as a ligand for REV-ERB. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, REV-ERB receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132738  Cd Length: 189  Bit Score: 38.63  E-value: 1.13e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A       49 MISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVeGILEIFDMLLATTSRFR 128
Cdd:cd06940  28 VVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKERSVTFLSGQKYSVDDLHSM-GAGDLLNSMFDFSEKLN 106

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U3S_A      129 ELKLQHKEYLCVKAMILLNSSMYPLvtatqdaDSSRKLAHLLNAVTDALVWVIAKsgiSSQQQSMRLANLLMLLSHVRHA 208
Cdd:cd06940 107 SLQLSDEEMGLFTAVVLVSADRSGL-------ENVNLVEALQETLIRALRTLIAK---NHPNEPSIFTKLLLKLPDLRTL 176

                       170
                ....*....|..
1U3S_A      209 SNKGMEHLLNMK 220
Cdd:cd06940 177 NNLHSEKLLAFK 188
NR_LBD_TR2_like cd06952
The ligand binding domain of the orphan nuclear receptors TR4 and TR2; The ligand binding ...
 50-83 6.95e-03

The ligand binding domain of the orphan nuclear receptors TR4 and TR2; The ligand binding domain of the TR4 and TR2 (human testicular receptor 4 and 2): TR4 and TR2 are orphan nuclear receptors. Several isoforms of TR4 and TR2 have been isolated in various tissues. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. The expression of TR2 is negatively regulated by androgen, retinoids, and radiation. The expression of both mouse TR2 and TR4 is up-regulated by neurocytokine ciliary neurotrophic factor (CNTF) in mouse. It has shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or TR4 include genes that are regulated by retinoic acid receptor, vitamin D receptor, peroxisome proliferator-activated receptor. TR4/2 binds to HREs as a dimer. Like other members of the nuclea r receptor (NR) superfamily of ligand-activated transcription factors, TR2-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132750  Cd Length: 222  Bit Score: 36.54  E-value: 6.95e-03
                        10        20        30
                ....*....|....*....|....*....|....
1U3S_A       50 ISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGL 83
Cdd:cd06952  38 IHWARSIPAFQALGAETQTSLVRACWPELFTLGL 71
NR_LBD_Dax1 cd07350
The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain; The ...
 40-83 8.64e-03

The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain; The ligand binding domain of the DAX1 protein: DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) is a nuclear receptor with a typical ligand binding domain, but lacks the DNA binding domain. DAX1 plays an important role in the normal development of several hormone-producing tissues. Duplications of the region of the X chromosome containing DAX1 cause dosage sensitive sex reversal. DAX1 acts as a global repressor of many nuclear receptors, including SF-1, LRH-1, ERR, ER, AR and PR. DAX1 can form homodimer and heterodimerizes with its alternatively spliced isoform DAX1A and other nuclear receptors such as SHP, ERalpha and SF-1.


Pssm-ID: 132764  Cd Length: 232  Bit Score: 36.34  E-value: 8.64e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
1U3S_A       40 KLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGL 83
Cdd:cd07350  26 KAASAVLVKTLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGL 69
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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