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Conserved domains on  [gi|732662980|ref|NP_001289964|]
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neuronal acetylcholine receptor subunit alpha-10 isoform b [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
LGIC_TM_cation cd19051
transmembrane domain of Cys-loop neurotransmitter-gated ion channels, includes 5HT3, nAChR, ...
33-118 1.51e-42

transmembrane domain of Cys-loop neurotransmitter-gated ion channels, includes 5HT3, nAChR, and ZAC; This superfamily contains the transmembrane (TM) domain of cationic Cys-loop neurotransmitter-gated ion channels, which include nicotinic acetylcholine receptor (nAChR), serotonin 5-hydroxytryptamine receptor (5-HT3), and zinc-activated ligand-gated ion channel (ZAC) receptor. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. The ligand-gated ion channels (LGICs) in this family are found across metazoans and have close homologs in bacteria. They are vital for communication throughout the nervous system. nAChR is a non-selective cation channel that is permeable to Na+ and K+, and some subunit combinations are also permeable to Ca2+. Na+ enters and K+ exits to allow net flow of positively charged ions inward. 5-HT3, a cation-selective channel, binds serotonin and is permeable to Na+, K+, and Ca2+. It mediates neuronal depolarization and excitation within the central and peripheral nervous systems. ZAC forms an ion channel gated by Zn2+, Cu2+, and H+ and is non-selectively permeable to monovalent cations. However, the role of ZAC in Zn2+, Cu2+, and H+ signaling require is as yet unknown.


:

Pssm-ID: 349853 [Multi-domain]  Cd Length: 112  Bit Score: 140.19  E-value: 1.51e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980  33 YVCNLLLPCVLISLLAPLAFHLPADSGEKVSLGVTVLLALTVFQLLLAESMPP-AESVPLIGKYYMATMTMVTFSTALTI 111
Cdd:cd19051    3 YVFNLILPCVLLSVLALLVFLLPPDSGEKVSLGITVLLSLTVFLLLVSESLPPtSDSVPLIGIYLLATMVLSALSTVLTV 82

                 ....*..
gi 732662980 112 LIMNLHY 118
Cdd:cd19051   83 IVLNLHH 89
Neur_chan_memb super family cl47784
Neurotransmitter-gated ion-channel transmembrane region; This family includes the four ...
37-228 2.29e-42

Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.


The actual alignment was detected with superfamily member pfam02932:

Pssm-ID: 460753 [Multi-domain]  Cd Length: 232  Bit Score: 143.56  E-value: 2.29e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980   37 LLLPCVLISLLAPLAFHLPADS-GEKVSLGVTVLLALTVFQLLLAESMPPAE-SVPLIGKYYMATMTMVTFSTALTILIM 114
Cdd:pfam02932   1 LIIPCVLISFLSWLVFWLPADAvGEKVTLGITVLLTMTVFLLLIRESLPKTSyVVPLIGKYLLFCMVFVFLSLVETVFVL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980  115 NLHYCGPSVRPVPAWARALLLGHLARGLCVRERGEPCGQSRPPE----------LSPSPQSPEGG-----AGPPAGPCHE 179
Cdd:pfam02932  81 NVHHRSPSTHKMPPWVRKIFLEKLPRLLGMKRPPEAPPPPASPGygskaeeyilRKPRSELPFEKqserhGLGRETTCSY 160
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980  180 PRCL-----------CRQEALLHHVATIANTFRSHRAAQRCHEDWKRLARVMDRFFLAIF 228
Cdd:pfam02932 161 GCSLgngssqprelsPELKKAVEGVNFIAKHLRSQDEYISVKEDWKYVAMVIDRLSRWIF 220
LGIC_ECD super family cl28912
extracellular domain (ECD) of Cys-loop neurotransmitter-gated ion channels (also known as ...
1-29 5.57e-13

extracellular domain (ECD) of Cys-loop neurotransmitter-gated ion channels (also known as ligand-gated ion channel (LGIC)); This superfamily contains the extracellular domain (ECD) of Cys-loop neurotransmitter-gated ion channels, which include nicotinic acetylcholine receptor (nAChR), serotonin 5-hydroxytryptamine receptor (5-HT3), type-A gamma-aminobutyric acid receptor (GABAAR) and glycine receptor (GlyR). These ligand-gated ion channels (LGICs) are found across metazoans and have close homologs in bacteria. They are vital for communication throughout the nervous system. GABAAR and GlyR are anionic channels, both mediating fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR receptor pore, resulting in hyperpolarization of the neuron. nAChR is a non-selective cation channel that is permeable to Na+ and K+, and some subunit combinations are also permeable to Ca2+. Na+ enters and K+ exits to allow net flow of positively charged ions inward. 5-HT3, a cation-selective channel, binds serotonin and is permeable to Na+, K+, and Ca2+. It mediates neuronal depolarization and excitation within the central and peripheral nervous systems. These ligand-gated chloride channels are critical not only for maintaining appropriate neuronal activity, but have long been important therapeutic targets: benzodiazepines, barbiturates, some intravenous and volatile anaesthetics, alcohol, strychnine, picrotoxin, and ivermectin all derive their biological activity from acting on the inhibitory half of the Cys-loop receptor family. The ECD contains the ligand binding sites for these receptors.


The actual alignment was detected with superfamily member cd19023:

Pssm-ID: 475126  Cd Length: 181  Bit Score: 65.01  E-value: 5.57e-13
                         10        20
                 ....*....|....*....|....*....
gi 732662980   1 MPARRRVLTYGCCSEPYPDVTFTLLLRRR 29
Cdd:cd19023  153 MPAKRNVITYGCCSEPYPDVTYTLLLKRR 181
 
Name Accession Description Interval E-value
LGIC_TM_cation cd19051
transmembrane domain of Cys-loop neurotransmitter-gated ion channels, includes 5HT3, nAChR, ...
33-118 1.51e-42

transmembrane domain of Cys-loop neurotransmitter-gated ion channels, includes 5HT3, nAChR, and ZAC; This superfamily contains the transmembrane (TM) domain of cationic Cys-loop neurotransmitter-gated ion channels, which include nicotinic acetylcholine receptor (nAChR), serotonin 5-hydroxytryptamine receptor (5-HT3), and zinc-activated ligand-gated ion channel (ZAC) receptor. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. The ligand-gated ion channels (LGICs) in this family are found across metazoans and have close homologs in bacteria. They are vital for communication throughout the nervous system. nAChR is a non-selective cation channel that is permeable to Na+ and K+, and some subunit combinations are also permeable to Ca2+. Na+ enters and K+ exits to allow net flow of positively charged ions inward. 5-HT3, a cation-selective channel, binds serotonin and is permeable to Na+, K+, and Ca2+. It mediates neuronal depolarization and excitation within the central and peripheral nervous systems. ZAC forms an ion channel gated by Zn2+, Cu2+, and H+ and is non-selectively permeable to monovalent cations. However, the role of ZAC in Zn2+, Cu2+, and H+ signaling require is as yet unknown.


Pssm-ID: 349853 [Multi-domain]  Cd Length: 112  Bit Score: 140.19  E-value: 1.51e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980  33 YVCNLLLPCVLISLLAPLAFHLPADSGEKVSLGVTVLLALTVFQLLLAESMPP-AESVPLIGKYYMATMTMVTFSTALTI 111
Cdd:cd19051    3 YVFNLILPCVLLSVLALLVFLLPPDSGEKVSLGITVLLSLTVFLLLVSESLPPtSDSVPLIGIYLLATMVLSALSTVLTV 82

                 ....*..
gi 732662980 112 LIMNLHY 118
Cdd:cd19051   83 IVLNLHH 89
Neur_chan_memb pfam02932
Neurotransmitter-gated ion-channel transmembrane region; This family includes the four ...
37-228 2.29e-42

Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.


Pssm-ID: 460753 [Multi-domain]  Cd Length: 232  Bit Score: 143.56  E-value: 2.29e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980   37 LLLPCVLISLLAPLAFHLPADS-GEKVSLGVTVLLALTVFQLLLAESMPPAE-SVPLIGKYYMATMTMVTFSTALTILIM 114
Cdd:pfam02932   1 LIIPCVLISFLSWLVFWLPADAvGEKVTLGITVLLTMTVFLLLIRESLPKTSyVVPLIGKYLLFCMVFVFLSLVETVFVL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980  115 NLHYCGPSVRPVPAWARALLLGHLARGLCVRERGEPCGQSRPPE----------LSPSPQSPEGG-----AGPPAGPCHE 179
Cdd:pfam02932  81 NVHHRSPSTHKMPPWVRKIFLEKLPRLLGMKRPPEAPPPPASPGygskaeeyilRKPRSELPFEKqserhGLGRETTCSY 160
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980  180 PRCL-----------CRQEALLHHVATIANTFRSHRAAQRCHEDWKRLARVMDRFFLAIF 228
Cdd:pfam02932 161 GCSLgngssqprelsPELKKAVEGVNFIAKHLRSQDEYISVKEDWKYVAMVIDRLSRWIF 220
LIC TIGR00860
Cation transporter family protein; The Ligand-gated Ion Channel (LIC) Family of ...
9-236 1.70e-41

Cation transporter family protein; The Ligand-gated Ion Channel (LIC) Family of Neurotransmitter Receptors TC 1.A.9)Members of the LIC family of ionotropic neurotransmitter receptors are found only in vertebrate and invertebrate animals. They exhibit receptor specificity for (1)acetylcholine, (2) serotonin, (3) glycine, (4) glutamate and (5) g-aminobutyric acid (GABA). All of these receptor channels are probably hetero- orhomopentameric. The best characterized are the nicotinic acetyl-choline receptors which are pentameric channels of a2bgd subunit composition. All subunits arehomologous. The three dimensional structures of the protein complex in both the open and closed configurations have been solved at 0.9 nm resolution.The channel protein complexes of the LIC family preferentially transport cations or anions depending on the channel (e.g., the acetylcholine receptors are cationselective while glycine receptors are anion selective). [Transport and binding proteins, Cations and iron carrying compounds]


Pssm-ID: 273305 [Multi-domain]  Cd Length: 459  Bit Score: 147.17  E-value: 1.70e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980    9 TYGCCSEPYPDVTFTLLLRRRAAAYVCNLLLPCVLISLLAPLAFHLPAD-SGEKVSLGVTVLLALTVFQLLLAESMPPAE 87
Cdd:TIGR00860 219 TSETNTGEYPCLTFSFVLRRRPLYYLLQLYIPSILIVILSWVSFWLPADaSGARVSLGITTLLTMTTFSSGVRESLPAVS 298
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980   88 SVPLIGKYYMATMTMVTFSTALTILIMNLHYCGPSVRPvpawaRALLLGHLARGLCVRERGEPCgqsRPPELSPSPQS-- 165
Cdd:TIGR00860 299 YVKAIDVYFAVCMAFVFLALLETAFVNYVHHKDPAQGK-----RHLLLERCAWRLCKQEPGEDY---RRPALDHASLSsv 370
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980  166 ---PEGGAGPPAGPCHEPRCL-----CRQEALLHHVAT---IANTFRSHRAAQRCHEDWKRLARVMDRFFLAIF------ 228
Cdd:TIGR00860 371 emrAKDGGRGLESPTERQRLLhspppAEGDLDLAGILEevrIAHRFRKRDESEEVVRDWKFRAKVIDKLSRMAFplafll 450

                  ....*...
gi 732662980  229 FSMALVMS 236
Cdd:TIGR00860 451 FNIGYWMS 458
LGIC_ECD_nAChR_A10 cd19023
extracellular domain of neuronal acetylcholine receptor subunit alpha 10 (CHRNA10); This ...
1-29 5.57e-13

extracellular domain of neuronal acetylcholine receptor subunit alpha 10 (CHRNA10); This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 10 (alpha10), encoded by the CHRNA10 gene. This protein is involved in cochlea hair cell development and is also expressed in the outer hair cells (OHCs) of the adult cochlea as well as in keratinocytes, the pituitary gland, B-cells, and T-cells. Unlike alpha9 nAChR subunits, alpha10 subunits do not generate functional channels when expressed heterologously, suggesting that alpha10 might serve as a structural subunit, much like a beta subunit of heteromeric receptors, providing only complementary components to the agonist binding site. Mammalian alpha10 subunits can form functional heteromeric alpha9alpha10 receptors, an atypical heteromeric receptor since it is composed only of alpha subunits compared to nAChRs typically assembled from alpha and beta subunits. A stoichiometry of (alpha9)2(alpha10)3 has been determined for the rat recombinant receptor. The alpha9alpha10 nAChR is an important therapeutic target for pain; selective block of alpha9alpha10 nicotinic acetylcholine receptors by the conotoxin RgIA has been shown to be analgesic in an animal model of nerve injury pain, and accelerates recovery of nerve function after injury, possibly through immune/inflammatory-mediated mechanisms.


Pssm-ID: 349824  Cd Length: 181  Bit Score: 65.01  E-value: 5.57e-13
                         10        20
                 ....*....|....*....|....*....
gi 732662980   1 MPARRRVLTYGCCSEPYPDVTFTLLLRRR 29
Cdd:cd19023  153 MPAKRNVITYGCCSEPYPDVTYTLLLKRR 181
Neur_chan_LBD pfam02931
Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ...
1-29 1.86e-05

Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.


Pssm-ID: 460752 [Multi-domain]  Cd Length: 215  Bit Score: 44.18  E-value: 1.86e-05
                          10        20
                  ....*....|....*....|....*....
gi 732662980    1 MPARRRVLTYGCCSEPYPDVTFTLLLRRR 29
Cdd:pfam02931 186 VPAKRREYPYGCYSELTGDVTFYFTLRRK 214
 
Name Accession Description Interval E-value
LGIC_TM_cation cd19051
transmembrane domain of Cys-loop neurotransmitter-gated ion channels, includes 5HT3, nAChR, ...
33-118 1.51e-42

transmembrane domain of Cys-loop neurotransmitter-gated ion channels, includes 5HT3, nAChR, and ZAC; This superfamily contains the transmembrane (TM) domain of cationic Cys-loop neurotransmitter-gated ion channels, which include nicotinic acetylcholine receptor (nAChR), serotonin 5-hydroxytryptamine receptor (5-HT3), and zinc-activated ligand-gated ion channel (ZAC) receptor. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. The ligand-gated ion channels (LGICs) in this family are found across metazoans and have close homologs in bacteria. They are vital for communication throughout the nervous system. nAChR is a non-selective cation channel that is permeable to Na+ and K+, and some subunit combinations are also permeable to Ca2+. Na+ enters and K+ exits to allow net flow of positively charged ions inward. 5-HT3, a cation-selective channel, binds serotonin and is permeable to Na+, K+, and Ca2+. It mediates neuronal depolarization and excitation within the central and peripheral nervous systems. ZAC forms an ion channel gated by Zn2+, Cu2+, and H+ and is non-selectively permeable to monovalent cations. However, the role of ZAC in Zn2+, Cu2+, and H+ signaling require is as yet unknown.


Pssm-ID: 349853 [Multi-domain]  Cd Length: 112  Bit Score: 140.19  E-value: 1.51e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980  33 YVCNLLLPCVLISLLAPLAFHLPADSGEKVSLGVTVLLALTVFQLLLAESMPP-AESVPLIGKYYMATMTMVTFSTALTI 111
Cdd:cd19051    3 YVFNLILPCVLLSVLALLVFLLPPDSGEKVSLGITVLLSLTVFLLLVSESLPPtSDSVPLIGIYLLATMVLSALSTVLTV 82

                 ....*..
gi 732662980 112 LIMNLHY 118
Cdd:cd19051   83 IVLNLHH 89
Neur_chan_memb pfam02932
Neurotransmitter-gated ion-channel transmembrane region; This family includes the four ...
37-228 2.29e-42

Neurotransmitter-gated ion-channel transmembrane region; This family includes the four transmembrane helices that form the ion channel.


Pssm-ID: 460753 [Multi-domain]  Cd Length: 232  Bit Score: 143.56  E-value: 2.29e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980   37 LLLPCVLISLLAPLAFHLPADS-GEKVSLGVTVLLALTVFQLLLAESMPPAE-SVPLIGKYYMATMTMVTFSTALTILIM 114
Cdd:pfam02932   1 LIIPCVLISFLSWLVFWLPADAvGEKVTLGITVLLTMTVFLLLIRESLPKTSyVVPLIGKYLLFCMVFVFLSLVETVFVL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980  115 NLHYCGPSVRPVPAWARALLLGHLARGLCVRERGEPCGQSRPPE----------LSPSPQSPEGG-----AGPPAGPCHE 179
Cdd:pfam02932  81 NVHHRSPSTHKMPPWVRKIFLEKLPRLLGMKRPPEAPPPPASPGygskaeeyilRKPRSELPFEKqserhGLGRETTCSY 160
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980  180 PRCL-----------CRQEALLHHVATIANTFRSHRAAQRCHEDWKRLARVMDRFFLAIF 228
Cdd:pfam02932 161 GCSLgngssqprelsPELKKAVEGVNFIAKHLRSQDEYISVKEDWKYVAMVIDRLSRWIF 220
LIC TIGR00860
Cation transporter family protein; The Ligand-gated Ion Channel (LIC) Family of ...
9-236 1.70e-41

Cation transporter family protein; The Ligand-gated Ion Channel (LIC) Family of Neurotransmitter Receptors TC 1.A.9)Members of the LIC family of ionotropic neurotransmitter receptors are found only in vertebrate and invertebrate animals. They exhibit receptor specificity for (1)acetylcholine, (2) serotonin, (3) glycine, (4) glutamate and (5) g-aminobutyric acid (GABA). All of these receptor channels are probably hetero- orhomopentameric. The best characterized are the nicotinic acetyl-choline receptors which are pentameric channels of a2bgd subunit composition. All subunits arehomologous. The three dimensional structures of the protein complex in both the open and closed configurations have been solved at 0.9 nm resolution.The channel protein complexes of the LIC family preferentially transport cations or anions depending on the channel (e.g., the acetylcholine receptors are cationselective while glycine receptors are anion selective). [Transport and binding proteins, Cations and iron carrying compounds]


Pssm-ID: 273305 [Multi-domain]  Cd Length: 459  Bit Score: 147.17  E-value: 1.70e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980    9 TYGCCSEPYPDVTFTLLLRRRAAAYVCNLLLPCVLISLLAPLAFHLPAD-SGEKVSLGVTVLLALTVFQLLLAESMPPAE 87
Cdd:TIGR00860 219 TSETNTGEYPCLTFSFVLRRRPLYYLLQLYIPSILIVILSWVSFWLPADaSGARVSLGITTLLTMTTFSSGVRESLPAVS 298
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980   88 SVPLIGKYYMATMTMVTFSTALTILIMNLHYCGPSVRPvpawaRALLLGHLARGLCVRERGEPCgqsRPPELSPSPQS-- 165
Cdd:TIGR00860 299 YVKAIDVYFAVCMAFVFLALLETAFVNYVHHKDPAQGK-----RHLLLERCAWRLCKQEPGEDY---RRPALDHASLSsv 370
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980  166 ---PEGGAGPPAGPCHEPRCL-----CRQEALLHHVAT---IANTFRSHRAAQRCHEDWKRLARVMDRFFLAIF------ 228
Cdd:TIGR00860 371 emrAKDGGRGLESPTERQRLLhspppAEGDLDLAGILEevrIAHRFRKRDESEEVVRDWKFRAKVIDKLSRMAFplafll 450

                  ....*...
gi 732662980  229 FSMALVMS 236
Cdd:TIGR00860 451 FNIGYWMS 458
LGIC_TM_nAChR cd19064
transmembrane domain of nicotinic acetylcholine receptor (nAChR); This family contains ...
33-118 2.71e-35

transmembrane domain of nicotinic acetylcholine receptor (nAChR); This family contains transmembrane (TM) domain of the nicotinic acetylcholine receptor (nAChR). The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. nAChR is found in high concentrations at the nerve-muscle synapse, where it mediates fast chemical transmission of electrical signals in response to the endogenous neurotransmitter acetylcholine (ACh) released from the nerve terminal into the synaptic cleft. Thus far, seventeen nAChR subunits have been identified, including ten alpha subunits, four beta subunits and one gamma, delta, and epsilon subunit each, all found on the cell membrane that non-selectively conducts cations (Na+, K+, Ca++). These nAChR subunits combine in several different ways to form functional nAChR subtypes which are broadly categorized as either muscle subtype located at the neuromuscular junction or neuronal subtype that are found on neurons and on other cell types throughout the body. The muscle type of nAChRs are formed by the alpha1, beta1, gamma, delta, and epsilon subunits while the neuronal type are composed of nine alpha subunits and three beta subunits, which combine in various permutations and combinations to form functional receptors. Among various subtypes of neuronal nAChRs, the homomeric alpha7 and the heteromeric alpha4beta2 receptors are the main subtypes widely distributed in the brain and implicated in the pathophysiology of neurodevelopmental disorders such as schizophrenia and autism and neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease. Among subtypes of muscle nAChRs, the heteromeric subunits (alpha1)2, beta, gamma, and delta in fetal muscle, and the gamma subunit replaced by epsilon in adult muscle have been implicated in congenital myasthenic syndromes and multiple pterygium syndromes due to various mutations. This family also includes alpha- and beta-like nAChRs found in protostomia.


Pssm-ID: 349866 [Multi-domain]  Cd Length: 113  Bit Score: 121.85  E-value: 2.71e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980  33 YVCNLLLPCVLISLLAPLAFHLPADSGEKVSLGVTVLLALTVFQLLLAESMPP-AESVPLIGKYYMATMTMVTFSTALTI 111
Cdd:cd19064    3 YTVNLIIPCVLISFLTVLVFYLPADSGEKITLSISVLLALTVFLLLIAEIIPPtSLVVPLIGKYLLFTMILVTLSIIVTV 82

                 ....*..
gi 732662980 112 LIMNLHY 118
Cdd:cd19064   83 IVLNVHH 89
LGIC_TM_5-HT3 cd19063
transmembrane domain of 5-hydroxytryptamine 3 (5-HT3) receptor; This family contains ...
33-116 3.80e-13

transmembrane domain of 5-hydroxytryptamine 3 (5-HT3) receptor; This family contains transmembrane (TM) domain of the serotonin 5-HT3 receptors. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. The 5-HT3 channel is cation-selective and mediates neuronal depolarization and excitation within the central and peripheral nervous systems. Like other ligand gated ion channels, the 5-HT3 receptor consists of five subunits arranged around a central ion conducting pore, which is permeable to Na+, K+, and Ca2+ ions. Binding of the neurotransmitter 5-hydroxytryptamine (serotonin) to the 5-HT3 receptor opens the channel, which then leads to an excitatory response in neurons, and the rapidly activating, desensitizing, inward current is predominantly carried by Na+ and K+ ions. This receptor is most closely related by homology to the nicotinic acetylcholine receptor (nAChR). Five subunits have been identified for this family: 5-HT3A, 5-HT3B, 5-HT3C, 5-HT3D, and 5-HT3E, encoded by HTR3A-E genes. Only 5-HT3A subunits are able to form functional homomeric receptors, whereas the 5-HT3B, C, D, and E subunits form heteromeric receptors with 5-HT3A. Different receptor subtypes are important mediators of nausea and vomiting during chemotherapy, pregnancy, and following surgery, while some contribute to neuro-gastroenterologic disorders such irritable bowel syndrome (IBS) and eating disorders as well as co-morbid psychiatric conditions. 5-HT3 receptor antagonists are established treatments for emesis and IBS, and are beneficial in the treatment of psychiatric diseases.


Pssm-ID: 349865  Cd Length: 121  Bit Score: 64.18  E-value: 3.80e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980  33 YVCNLLLPCVLISLLAPLAFHLPADSGEKVSLGVTVLLALTVFQLLLAESMPP-AESVPLIGKYYMATMTMVTFSTALTI 111
Cdd:cd19063    3 YVVNLLIPSIFLMLVDLASFYLPPNSGERLGFKVTLLLGYSVFLLILNDLLPAtAIGTPLIGVYFVVCLALMVLSLLETI 82

                 ....*
gi 732662980 112 LIMNL 116
Cdd:cd19063   83 LIVKL 87
LGIC_ECD_nAChR_A10 cd19023
extracellular domain of neuronal acetylcholine receptor subunit alpha 10 (CHRNA10); This ...
1-29 5.57e-13

extracellular domain of neuronal acetylcholine receptor subunit alpha 10 (CHRNA10); This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 10 (alpha10), encoded by the CHRNA10 gene. This protein is involved in cochlea hair cell development and is also expressed in the outer hair cells (OHCs) of the adult cochlea as well as in keratinocytes, the pituitary gland, B-cells, and T-cells. Unlike alpha9 nAChR subunits, alpha10 subunits do not generate functional channels when expressed heterologously, suggesting that alpha10 might serve as a structural subunit, much like a beta subunit of heteromeric receptors, providing only complementary components to the agonist binding site. Mammalian alpha10 subunits can form functional heteromeric alpha9alpha10 receptors, an atypical heteromeric receptor since it is composed only of alpha subunits compared to nAChRs typically assembled from alpha and beta subunits. A stoichiometry of (alpha9)2(alpha10)3 has been determined for the rat recombinant receptor. The alpha9alpha10 nAChR is an important therapeutic target for pain; selective block of alpha9alpha10 nicotinic acetylcholine receptors by the conotoxin RgIA has been shown to be analgesic in an animal model of nerve injury pain, and accelerates recovery of nerve function after injury, possibly through immune/inflammatory-mediated mechanisms.


Pssm-ID: 349824  Cd Length: 181  Bit Score: 65.01  E-value: 5.57e-13
                         10        20
                 ....*....|....*....|....*....
gi 732662980   1 MPARRRVLTYGCCSEPYPDVTFTLLLRRR 29
Cdd:cd19023  153 MPAKRNVITYGCCSEPYPDVTYTLLLKRR 181
LGIC_ECD_nAChR_A9 cd19022
extracellular domain of neuronal acetylcholine receptor subunit alpha 9 (CHRNA9); This ...
1-30 1.47e-12

extracellular domain of neuronal acetylcholine receptor subunit alpha 9 (CHRNA9); This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 9 (alpha9), encoded by the CHRNA9 gene. This protein is involved in cochlea hair cell development and is also expressed in the outer hair cells (OHCs) of the adult cochlea as well as in keratinocytes, the pituitary gland, B-cells, and T-cells. Mammalian alpha9 subunits can form functional homomeric alpha9 receptors as well as the heteromeric alpha9alpha10 receptors, the latter being atypical since the heteromeric alpha9alpha10 receptor is composed only of alpha subunits compared to nAChRs typically assembled from alpha and beta subunits. A stoichiometry of (alpha9)2(alpha10)3 has been determined for the rat recombinant receptor. The alpha9alpha10 nAChR is an important therapeutic target for pain; selective block of alpha9alpha10 nicotinic acetylcholine receptors by the conotoxin RgIA has been shown to be analgesic in an animal model of nerve injury pain, and accelerates recovery of nerve function after injury, possibly through immune/inflammatory-mediated mechanisms. CHRNA9 polymorphisms are associated with non-small cell lung cancer, and effect of a particular SNP (rs73229797) and passive smoking exposure on risk of breast malignancy has been observed.


Pssm-ID: 349823  Cd Length: 207  Bit Score: 64.68  E-value: 1.47e-12
                         10        20        30
                 ....*....|....*....|....*....|
gi 732662980   1 MPARRRVLTYGCCSEPYPDVTFTLLLRRRA 30
Cdd:cd19022  178 MPAVKNVITYGCCSEPYPDVTFTLILKRRS 207
LGIC_TM cd03559
transmembrane domain of Cys-loop neurotransmitter-gated ion channels; This superfamily ...
33-123 4.28e-12

transmembrane domain of Cys-loop neurotransmitter-gated ion channels; This superfamily contains the transmembrane domain of Cys-loop neurotransmitter-gated ion channels, which include nicotinic acetylcholine receptor (nAChR), serotonin 5-hydroxytryptamine receptor (5-HT3), type-A gamma-aminobutyric acid receptor (GABAAR), and glycine receptor (GlyR). These ligand-gated ion channels (LGICs) are found across metazoans and have close homologs in bacteria. They are vital for communication throughout the nervous system where the sign of synaptic connections (excitatory or inhibitory) is determined by the charge of the ions that flow through these channels. In general, channels that conduct positive ions are excitatory, whereas channels that conduct negative ions are inhibitory. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. GABAAR and GlyR are anionic channels, both mediating fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR receptor pore, resulting in hyperpolarization of the neuron. nAChR is a non-selective cation channel that is permeable to Na+ and K+, and some subunit combinations are also permeable to Ca2+. Na+ enters and K+ exits to allow net flow of positively charged ions inward. 5-HT3, a cation-selective channel, binds serotonin and is permeable to Na+, K+, and Ca2+. It mediates neuronal depolarization and excitation within the central and peripheral nervous systems. These ligand-gated chloride channels are critical not only for maintaining appropriate neuronal activity, but have long been important therapeutic targets: benzodiazepines, barbiturates, some intravenous and volatile anaesthetics, alcohol, strychnine, picrotoxin, and ivermectin all derive their biological activity from acting on the inhibitory half of the Cys-loop receptor family.


Pssm-ID: 349850  Cd Length: 116  Bit Score: 61.01  E-value: 4.28e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980  33 YVCNLLLPCVLISLLAPLAFHLPADSGEKVSLGVTVLLALTVFQLLLAESMPPAESVPLIGKYYMATMTMVTFSTALTIL 112
Cdd:cd03559    2 YAVSLLLPSILIMVVSWVGFWLPPDSGERVSFKITLLLTYSVFLIIVSDTLPATPYTPLIDVYFVVCMALLFIALLETIF 81
                         90
                 ....*....|.
gi 732662980 113 IMNLHYCGPSV 123
Cdd:cd03559   82 IVRLVHKQDRV 92
LGIC_ECD_nAChR cd18997
extracellular domain of nicotinic acetylcholine receptor; This family contains the ...
1-29 1.22e-10

extracellular domain of nicotinic acetylcholine receptor; This family contains the extracellular domain of nicotinic acetylcholine receptor (nAChR), a member of the pentameric "Cys-loop" superfamily of transmitter-gated ion channels. nAChR is found in high concentrations at the nerve-muscle synapse, where it mediates fast chemical transmission of electrical signals in response to the endogenous neurotransmitter acetylcholine (ACh) released from the nerve terminal into the synaptic cleft. Thus far, seventeen nAChR subunits have been identified, including ten alpha subunits, four beta subunits, and one gamma, delta, and epsilon subunit each, all found on the cell membrane that non-selectively conducts cations (Na+, K+, Ca++). These nAChR subunits combine in several different ways to form functional nAChR subtypes which are broadly categorized as either muscle subtype located at the neuromuscular junction or neuronal subtype that are found on neurons and on other cell types throughout the body. The muscle type of nAChRs are formed by the alpha1, beta1, gamma, delta, and epsilon subunits while the neuronal type are composed of nine alpha subunits and three beta subunits, which combine in various permutations and combinations to form functional receptors. Among various subtypes of neuronal nAChRs, the homomeric alpha7 and the heteromeric alpha4beta2 receptors are the main subtypes widely distributed in the brain and implicated in the pathophysiology of neurodevelopmental disorders such as schizophrenia and autism and neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease. Among subtypes of muscle nAChRs, the heteromeric subunits (alpha1)2, beta, gamma, and delta in fetal muscle, and the gamma subunit replaced by epsilon in adult muscle have been implicated in congenital myasthenic syndromes and multiple pterygium syndromes due to various mutations. This family also includes alpha- and beta-like nAChRs found in protostomia.


Pssm-ID: 349798  Cd Length: 181  Bit Score: 58.66  E-value: 1.22e-10
                         10        20
                 ....*....|....*....|....*....
gi 732662980   1 MPARRRVLTYGCCSEPYPDVTFTLLLRRR 29
Cdd:cd18997  153 APAKRNVVKYSCCPEPYPDVTFTIHIRRK 181
LGIC_ECD_nAChR_proto_alpha-like cd19031
extracellular domain of nicotinic acetylcholine receptor subunit alpha-like found in ...
2-29 2.13e-08

extracellular domain of nicotinic acetylcholine receptor subunit alpha-like found in protostomia; This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha-like in organisms that include arthropods, mollusks, annelid worms, and flat worms, and have their cholinergic system limited to the central nervous system. C. elegans genome encodes 29 acetylcholine receptor subunits, of which the levamisole-sensitive receptor (L-AChR) alpha-subunits, UNC-38, UNC-63, and LEV-8, included in this subfamily, form heteromers with the two non-alpha (also known as beta-like) subunits, UNC-29 and LEV-1. This receptor functions as the main excitatory postsynaptic receptor at neuromuscular junctions, indicating that many are expressed in neurons. Also included is the nicotinic alpha subunit MARA1 (Manduca ACh Receptor Alpha 1) which is expressed in Ca2+ responding neurons and contributes to the nicotinic responses in the neurons. In insects, the receptors supply fast synaptic excitatory transmission and represent a major target for several insecticides. In Drosophila, ten exclusively neuronal nAChRs have been identified, Dalpha1-Dalpha7 and Dbeta1-Dbeta3, and various combinations of these subunits and mutations are key to nAChR function. Alpha5 subunit is involved in alpha-bungarotoxin sensitivity while the alpha6 subunit is essential for the insecticidal effect of spinosad. nAChR agonists acetylcholine, nicotine, and neonicotinoids stimulate dopamine release in Drosophila larval ventral nerve cord and mutations in nAChR subunits affect how insecticides stimulate dopamine release.


Pssm-ID: 349832  Cd Length: 222  Bit Score: 53.05  E-value: 2.13e-08
                         10        20
                 ....*....|....*....|....*...
gi 732662980   2 PARRRVLTYGCCSEPYPDVTFTLLLRRR 29
Cdd:cd19031  192 PARRNEKYYPCCDEPYPDITFNITLRRK 219
LGIC_ECD_nAChR_proto-like cd19033
nicotinic acetylcholine receptor (nAChR) subunit extracellular domain in molluscs and annelids; ...
2-29 9.31e-08

nicotinic acetylcholine receptor (nAChR) subunit extracellular domain in molluscs and annelids; This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit found in molluscs, including several Lymnaea nAChRs, and annelids that are mostly uncharacterized. To date, 12 Lymnaea nAChRs have been identified which can be subdivided in two subtypes according to the residues that may be contributing to the selectivity of ion conductance. Phylogenetic analysis of the nAChR gene sequences suggests that anionic nAChRs in molluscs probably evolved from cationic ancestors through amino acid substitutions in the ion channel pore which is a mechanism different from acetylcholine-gated channels in other invertebrates.


Pssm-ID: 349834  Cd Length: 183  Bit Score: 50.75  E-value: 9.31e-08
                         10        20
                 ....*....|....*....|....*...
gi 732662980   2 PARRRVLTYGCCSEPYPDVTFTLLLRRR 29
Cdd:cd19033  156 PAVKNVKYYPCCPEPYPDLTFFLVIKRR 183
LGIC_ECD_nAChR_A7 cd19020
extracellular domain of neuronal acetylcholine receptor subunit alpha 7 (CHRNA7); This ...
1-29 6.08e-07

extracellular domain of neuronal acetylcholine receptor subunit alpha 7 (CHRNA7); This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 7 (alpha7), encoded by the CHRNA7 gene. Alpha7 subunits form a homo-pentameric channel, displays marked permeability to calcium ions and is a major component of brain nicotinic receptors that are blocked by, and highly sensitive to, alpha-bungarotoxin. This protein is ubiquitously expressed in both the central nervous system and in the periphery, in several tissues, including adrenal, small intestine, testis, and stomach. CHRNA7 is located in a region identified as a major susceptibility locus for juvenile myoclonic epilepsy and a chromosomal location involved in the genetic transmission of schizophrenia. It is also genetically linked to other disorders with cognitive deficits, including bipolar disorder, ADHD, Alzheimer's disease, and Rett syndrome. An evolutionarily recent partial duplication of CHRNA7 on chromosome 15 forms a new gene, CHRFAM7A or FAM7A, which encodes the protein dup-alpha7. This protein assembles with alpha7 subunits, results in fewer binding sites and is a dominant negative regulator of alpha7 nAChR function.


Pssm-ID: 349821 [Multi-domain]  Cd Length: 180  Bit Score: 48.45  E-value: 6.08e-07
                         10        20
                 ....*....|....*....|....*....
gi 732662980   1 MPARRRVLTYGCCSEPYPDVTFTLLLRRR 29
Cdd:cd19020  152 VPGKRNEKFYECCKEPYPDVTFTVTMRRR 180
LGIC_ECD_nAChR_A7L cd19021
extracellular domain of neuronal acetylcholine receptor subunit alpha-7-like; This family ...
1-29 2.39e-06

extracellular domain of neuronal acetylcholine receptor subunit alpha-7-like; This family contains the extracellular domain of nicotinic acetylcholine receptor (nAChR), a member of the pentameric "Cys-loop" superfamily of transmitter-gated ion channels. nAChR is found in high concentrations at the nerve-muscle synapse, where it mediates fast chemical transmission of electrical signals in response to the endogenous neurotransmitter acetylcholine (ACh) released from the nerve terminal into the synaptic cleft. Thus far, seventeen nAChR subunits have been identified, including ten alpha subunits, four beta subunits and one gamma, delta, and epsilon subunit each, all found on the cell membrane that non-selectively conducts cations (Na+, K+, Ca++). These nAChR subunits combine in several different ways to form functional nAChR subtypes which are broadly categorized as either muscle subtype located at the neuromuscular junction or neuronal subtype that are found on neurons and on other cell types throughout the body. The muscle type of nAChRs are formed by the alpha1, beta1, gamma, delta, and epsilon subunits while the neuronal type are composed of nine alpha subunits and three beta subunits, which combine in various permutations and combinations to form functional receptors. Among various subtypes of neuronal nAChRs, the homomeric alpha7 and the heteromeric alpha4beta2 receptors are the main subtypes widely distributed in the brain and implicated in the pathophysiology of neurodevelopmental disorders such as schizophrenia and autism and neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease.


Pssm-ID: 349822 [Multi-domain]  Cd Length: 179  Bit Score: 46.57  E-value: 2.39e-06
                         10        20
                 ....*....|....*....|....*....
gi 732662980   1 MPARRRVLTYGCCSEPYPDVTFTLLLRRR 29
Cdd:cd19021  151 VPGKRNELYYECCKEPYPDVTYTITMRRR 179
Neur_chan_LBD pfam02931
Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ...
1-29 1.86e-05

Neurotransmitter-gated ion-channel ligand binding domain; This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.


Pssm-ID: 460752 [Multi-domain]  Cd Length: 215  Bit Score: 44.18  E-value: 1.86e-05
                          10        20
                  ....*....|....*....|....*....
gi 732662980    1 MPARRRVLTYGCCSEPYPDVTFTLLLRRR 29
Cdd:pfam02931 186 VPAKRREYPYGCYSELTGDVTFYFTLRRK 214
LGIC_TM_bact cd19050
transmembrane domain of prokaryotic pentameric ligand-gated ion channels (pLGIC); This family ...
33-142 4.70e-05

transmembrane domain of prokaryotic pentameric ligand-gated ion channels (pLGIC); This family contains transmembrane (TM) domain of bacterial pentameric ligand-gated ion channels (pLGICs) including ones from Gloeobacter violaceus (GLIC) and Erwinia chrysanthemi (ELIC). The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. Studies show that GLIC activation is inhibited by most general anaesthetics at clinical concentrations, including xenon which has been used in clinical practice as a potent gaseous anesthetic for decades. Xenon binding sites have been identified in three distinct regions of the TMD: in a large intra-subunit cavity, in the pore, and at the interface between adjacent subunits. Propofol, the drug used for induction and maintenance of general anesthesia, and desflurane, a negative allosteric modulator of GLIC bind at the entrance in the intra-subunit cavity. Alzheimer's drug memantine, which blocks ion conduction at vertebrate pLGICs by plugging the channel pore, has been shown to have similar potency in ELIC.


Pssm-ID: 349852  Cd Length: 119  Bit Score: 41.81  E-value: 4.70e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732662980  33 YVCNLLLPCVLISLLAPLAFHL-PADSGEKVSLGVTVLLALTVFQLLLAESMPPAESVPLIGKYYMATMTMVTFSTALTI 111
Cdd:cd19050    2 YIWKVILPLLLIVAMSWSVFWIdPESFGPQIGISVTSMLTLIAFNFLISNSLPRLPYLTFMDAFILASYLLVFLALIEVI 81
                         90       100       110
                 ....*....|....*....|....*....|.
gi 732662980 112 LIMNLHYCGPSvrpvpawARALLLGHLARGL 142
Cdd:cd19050   82 VTHYLARNGKE-------ALALRIDRISRWA 105
LGIC_TM_GABAAR_beta cd19053
transmembrane domain of beta subunits of type-A gamma-aminobutyric acid receptor (GABAAR); ...
33-103 1.18e-04

transmembrane domain of beta subunits of type-A gamma-aminobutyric acid receptor (GABAAR); This family contains transmembrane (TM) domain of the beta subunit of type-A beta-aminobutyric acid receptor (GABAAR), which includes beta1-beta4 in vertebrates. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. Mutations or genetic variations of the genes encoding beta2 (GABRB2) and beta3 (GABRB3) have been associated with human epilepsy, both with and without febrile seizures. Mutations in GABRB2, and GABRB3 have been associated with infantile spasms and Lennox-Gastaut syndrome. A de novo missense mutation of GABRB2 causes early myoclonic encephalopathy, a disease with a devastating prognosis, characterized by neonatal onset of seizures. Another de novo heterozygous missense variant in exon 4 of GABRB2 is associated with intellectual disability and epilepsy. Mutations in the GABRB1 gene encoding beta1 promote alcohol consumption through increased tonic inhibition.


Pssm-ID: 349855  Cd Length: 111  Bit Score: 40.33  E-value: 1.18e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 732662980  33 YVCNLLLPCVLISLLAPLAFHLPAD-SGEKVSLGVTVLLALTVFQLLLAESMPPAESVPLIGKYYMATMTMV 103
Cdd:cd19053    2 FILQTYMPSILITILSWVSFWINYDaSAARVALGITTVLTMTTINTHLRETLPKIPYVKAIDMYLMGCFVFV 73
LGIC_TM_anion cd19049
transmembrane domain of anionic Cys-loop neurotransmitter-gated ion channels, includes GABAAR, ...
39-106 1.38e-04

transmembrane domain of anionic Cys-loop neurotransmitter-gated ion channels, includes GABAAR, GlyR and GluCl; This family contains transmembrane domain of type-A gamma-aminobutyric acid receptor (GABAAR) as well as glycine receptor (GlyR) subunits. Thus far, there are 18 vertebrate receptor subunits categorized in 7 families: alpha1-6, beta1-4, gamma1-4, delta, epsilon, theta, rho, and pi. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. GlyR, with a similar structure as GABAAR, is concentrated in the brain stem and spinal cord in the CNS and can be activated by glycine, beta-alanine, or taurine. It is selectively blocked by the high-affinity competitive antagonist strychnine, which causes death by asphyxiation. An autosomal dominant R271Q mutation in GLRA1 causes hyperekplexia (Startle disease or Stiff Baby Syndrome) by decreasing glycine sensitivity.


Pssm-ID: 349851  Cd Length: 111  Bit Score: 40.13  E-value: 1.38e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 732662980  39 LPCVLISLLAPLAFHLPADS-GEKVSLGVTVLLALTVFQLLLAESMPPAESVPLIGKYYMATMTMVTFS 106
Cdd:cd19049    8 IPSILIVILSWVSFWIDPEAvPARVSLGITTVLTMTTQSSGVRSSLPKVSYVKAIDVWLGVCFVFVFAA 76
LGIC_AChBP cd18995
acetylcholine binding protein (AChBP); This family contains acetylcholine binding protein ...
3-29 1.50e-04

acetylcholine binding protein (AChBP); This family contains acetylcholine binding protein (AChBP) which is a soluble extracellular domain homolog secreted by protostomia, and has been widely recognized as a surrogate for the ligand binding domain of nicotinic acetylcholine receptors (nAChRs). AChBP forms a pentameric structure where the interfaces between the subunits provide an acetylcholine (ACh) binding pocket homologous to the binding pocket of nAChRs. Thus far, AChBPs have been characterized only in aquatic mollusks, which have shown low sensitivity to neonicotinoids, the insecticides targeting insect nAChRs. Lymnaea stagnalis acetylcholine binding protein (Ls-AChBP) which has been found in glial cells as a water-soluble protein modulating synaptic ACh concentration has its the binding pocket show better resemblance as it contains all the five aromatic residues fully conserved in nAChR. Five AChBP subunits have been characterized in Pardosa pseudoannulata, a predator enemy against rice insect pests, and share higher sequence similarities with nAChR subunits of both insects and mammals compared with mollusk AChBP subunits.


Pssm-ID: 349796  Cd Length: 180  Bit Score: 41.19  E-value: 1.50e-04
                         10        20
                 ....*....|....*....|....*..
gi 732662980   3 ARRRVLTYGCCSEPYPDVTFTLLLRRR 29
Cdd:cd18995  154 QKREVKTYSCCPEPYPDIEFVFTFKKR 180
 
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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