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Conserved domains on  [gi|2090556656|pdb|7D69|A]
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Chain A, Histone H3

Protein Classification

histone H3/H4 domain-containing protein( domain architecture ID 581047)

histone H3/H4 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HFD_SF super family cl45933
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 4-137 3.58e-53

histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally conserved interaction motif involved in heterodimerization of the core histones and their assembly into the nucleosome octamer. Histone fold heterodimers play crucial roles in gene regulation. The minimal HFD consists of three alpha helices connected by two short, unstructured loops. The HFD is found in core histones, TATA box-binding protein-associated factors (TAFs), and many other transcription factors. HFD plays a role in the nucleosomal core particle by conserving histone interactions; these contain more than one HFD. The structure of the nucleosome core particle has two modes that have the largest interaction surfaces, and these are the H3-H4 and H2A-H2B heterodimer interactions. Several TAFs interact via histone-fold (HF) motifs. Five HF-containing TAF pairs have been described in transcription factor II D (TFIID): TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10.


The actual alignment was detected with superfamily member PTZ00018:

Pssm-ID: 480273 [Multi-domain]  Cd Length: 136  Bit Score: 164.69  E-value: 3.58e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
7D69_A         4 MARTKHTARKTTSAtKAPRKTIARKAARKTASSTSGIKKTGRKKQGMVAVKEIKKYQKSTDLLIRKLPFSKLVRDIVTSg 83
Cdd:PTZ00018   1 MARTKQTARKSTGG-KAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQD- 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
7D69_A        84 lSKSDIRFQGAAVEALQESAENYIISLFVDTQLCAEHAKRVTIMKPDMELATRI 137
Cdd:PTZ00018  79 -FKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 4-137 3.58e-53

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 164.69  E-value: 3.58e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
7D69_A         4 MARTKHTARKTTSAtKAPRKTIARKAARKTASSTSGIKKTGRKKQGMVAVKEIKKYQKSTDLLIRKLPFSKLVRDIVTSg 83
Cdd:PTZ00018   1 MARTKQTARKSTGG-KAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQD- 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
7D69_A        84 lSKSDIRFQGAAVEALQESAENYIISLFVDTQLCAEHAKRVTIMKPDMELATRI 137
Cdd:PTZ00018  79 -FKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 45-137 2.91e-46

histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication, and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called the histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.


Pssm-ID: 467036  Cd Length: 95  Bit Score: 145.37  E-value: 2.91e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
7D69_A       45 RKKQGMVAVKEIKKYQKSTDLLIRKLPFSKLVRDIVTSgLSKSDIRFQGAAVEALQESAENYIISLFVDTQLCAEHAKRV 124
Cdd:cd22911   2 RYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQD-FKTKDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRV 80

                        90
                ....*....|...
7D69_A      125 TIMKPDMELATRI 137
Cdd:cd22911  81 TLMPKDMQLARRI 93
H3 smart00428
Histone H3;
38-137 1.23e-39

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 129.10  E-value: 1.23e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
7D69_A          38 SGIKKTGRKKQGMVAVKEIKKYQKSTDLLIRKLPFSKLVRDIVTSGLSKSDIRFQGAAVEALQESAENYIISLFVDTQLC 117
Cdd:smart00428   1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLL 80

                           90       100
                   ....*....|....*....|
7D69_A         118 AEHAKRVTIMKPDMELATRI 137
Cdd:smart00428  81 AIHAKRVTIMPKDIQLARRI 100
Histone pfam00125
Core histone H2A/H2B/H3/H4;
4-137 5.91e-33

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 112.91  E-value: 5.91e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
7D69_A          4 MARTKHTARKTTSaTKAPRKTIARKAARKTasstsgIKKTGRKKQGMVAVKEIKKYQKSTDLLIRKLPFSKLVRDIVTSG 83
Cdd:pfam00125   1 MARNKNKANPRRG-GTAPEKKISQKSSSSS------KKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQST 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
7D69_A         84 lsKSDIRFQGAAVEALQESAENYIISLFVDTQLCAEHAKRVTIMKPDMELATRI 137
Cdd:pfam00125  74 --KTDLRISADAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRL 125
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 4-137 3.58e-53

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 164.69  E-value: 3.58e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
7D69_A         4 MARTKHTARKTTSAtKAPRKTIARKAARKTASSTSGIKKTGRKKQGMVAVKEIKKYQKSTDLLIRKLPFSKLVRDIVTSg 83
Cdd:PTZ00018   1 MARTKQTARKSTGG-KAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQD- 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
7D69_A        84 lSKSDIRFQGAAVEALQESAENYIISLFVDTQLCAEHAKRVTIMKPDMELATRI 137
Cdd:PTZ00018  79 -FKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131
PLN00121 PLN00121
histone H3; Provisional
 4-137 1.38e-46

histone H3; Provisional


Pssm-ID: 177733 [Multi-domain]  Cd Length: 136  Bit Score: 147.89  E-value: 1.38e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
7D69_A         4 MARTKHTARKTTSAtKAPRKTIARKAARKTASSTSGIKKTGRKKQGMVAVKEIKKYQKSTDLLIRKLPFSKLVRDIVTSg 83
Cdd:PLN00121   1 MARTKQTARKSTGG-KAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQD- 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
7D69_A        84 lSKSDIRFQGAAVEALQESAENYIISLFVDTQLCAEHAKRVTIMKPDMELATRI 137
Cdd:PLN00121  79 -FKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 45-137 2.91e-46

histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication, and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called the histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.


Pssm-ID: 467036  Cd Length: 95  Bit Score: 145.37  E-value: 2.91e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
7D69_A       45 RKKQGMVAVKEIKKYQKSTDLLIRKLPFSKLVRDIVTSgLSKSDIRFQGAAVEALQESAENYIISLFVDTQLCAEHAKRV 124
Cdd:cd22911   2 RYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQD-FKTKDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRV 80

                        90
                ....*....|...
7D69_A      125 TIMKPDMELATRI 137
Cdd:cd22911  81 TLMPKDMQLARRI 93
H3 smart00428
Histone H3;
38-137 1.23e-39

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 129.10  E-value: 1.23e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
7D69_A          38 SGIKKTGRKKQGMVAVKEIKKYQKSTDLLIRKLPFSKLVRDIVTSGLSKSDIRFQGAAVEALQESAENYIISLFVDTQLC 117
Cdd:smart00428   1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLL 80

                           90       100
                   ....*....|....*....|
7D69_A         118 AEHAKRVTIMKPDMELATRI 137
Cdd:smart00428  81 AIHAKRVTIMPKDIQLARRI 100
Histone pfam00125
Core histone H2A/H2B/H3/H4;
4-137 5.91e-33

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 112.91  E-value: 5.91e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
7D69_A          4 MARTKHTARKTTSaTKAPRKTIARKAARKTasstsgIKKTGRKKQGMVAVKEIKKYQKSTDLLIRKLPFSKLVRDIVTSG 83
Cdd:pfam00125   1 MARNKNKANPRRG-GTAPEKKISQKSSSSS------KKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQST 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
7D69_A         84 lsKSDIRFQGAAVEALQESAENYIISLFVDTQLCAEHAKRVTIMKPDMELATRI 137
Cdd:pfam00125  74 --KTDLRISADAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRL 125
PLN00161 PLN00161
histone H3; Provisional
 4-137 6.74e-31

histone H3; Provisional


Pssm-ID: 215082 [Multi-domain]  Cd Length: 135  Bit Score: 107.78  E-value: 6.74e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
7D69_A         4 MARTKHTarKTTSATKAPRKTIARKAARKTAsstsgiKKTGRKKQGMVAVKEIKKYQKSTDLLIRKLPFSKLVRDIvTSG 83
Cdd:PLN00161   1 MARRLQG--KRFRKGKKPQKEASGVTRQELD------KKPHRYRPGTVALREIRKYQKSTELLIRKLPFARLVREI-SNE 71

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
7D69_A        84 LSKSDIRFQGAAVEALQESAENYIISLFVDTQLCAEHAKRVTIMKPDMELATRI 137
Cdd:PLN00161  72 MLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRI 125
PLN00160 PLN00160
histone H3; Provisional
 47-137 4.33e-30

histone H3; Provisional


Pssm-ID: 165727  Cd Length: 97  Bit Score: 104.74  E-value: 4.33e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
7D69_A        47 KQGMVAVKEIKKYQKSTDLLIRKLPFSKLVRDIvTSGLSKSDIRFQGAAVEALQESAENYIISLFVDTQLCAEHAKRVTI 126
Cdd:PLN00160   2 RPGEKALKEIKMYQKSTDLLIRRLPFARLVREI-QMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTI 80

                         90
                 ....*....|.
7D69_A       127 MKPDMELATRI 137
Cdd:PLN00160  81 MPKDMQLARRI 91
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 88-134 5.23e-04

histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally conserved interaction motif involved in heterodimerization of the core histones and their assembly into the nucleosome octamer. Histone fold heterodimers play crucial roles in gene regulation. The minimal HFD consists of three alpha helices connected by two short, unstructured loops. The HFD is found in core histones, TATA box-binding protein-associated factors (TAFs), and many other transcription factors. HFD plays a role in the nucleosomal core particle by conserving histone interactions; these contain more than one HFD. The structure of the nucleosome core particle has two modes that have the largest interaction surfaces, and these are the H3-H4 and H2A-H2B heterodimer interactions. Several TAFs interact via histone-fold (HF) motifs. Five HF-containing TAF pairs have been described in transcription factor II D (TFIID): TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10.


Pssm-ID: 467021  Cd Length: 63  Bit Score: 36.43  E-value: 5.23e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
7D69_A       88 DIRFQGAAVEALQESAENYIISLFVDTQLCAEHAKRVTIMKPDMELA 134
Cdd:cd00076  15 FDSVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELA 61
valS PRK14900
valyl-tRNA synthetase; Provisional
 8-47 1.48e-03

valyl-tRNA synthetase; Provisional


Pssm-ID: 237855 [Multi-domain]  Cd Length: 1052  Bit Score: 37.66  E-value: 1.48e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
7D69_A          8 KHTARKTTSATKAPRKTIARKAARKTASSTSGIKKTGRKK 47
Cdd:PRK14900 1013 KKAAAKKKVAKKAPAKKVARKPAAKKAAKKPARKAAGRKA 1052
HFD_CENP-T cd22920
histone-fold domain found in centromere protein T (CENP-T) and similar proteins; CENP-T, also ...
 73-133 7.50e-03

histone-fold domain found in centromere protein T (CENP-T) and similar proteins; CENP-T, also called interphase centromere complex protein 22 (ICEN22), is a component of the CENPA-NAC (nucleosome-associated) complex, which plays a central role in the assembly of kinetochore proteins, mitotic progression, and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres. CENP-T is also part of a nucleosome-associated complex that binds specifically to histone H3-containing nucleosomes at the centromere, as opposed to nucleosomes containing CENPA. Moreover, CENP-T is a component of the heterotetrameric CENP-T-W-S-X complex that binds and supercoils DNA, and plays an important role in kinetochore assembly. CENP-T has a fundamental role in kinetochore assembly and function. It is one of the inner kinetochore proteins, with most further proteins binding downstream. It is required for normal chromosome organization and normal progress through mitosis.


Pssm-ID: 467045  Cd Length: 94  Bit Score: 34.07  E-value: 7.50e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
7D69_A       73 SKLVRDIVTSglsKSDIRFQGAAVEALQESAENYIISLFVDTQLCAEHAKRVTIMKPDMEL 133
Cdd:cd22920   5 KSLVKKLFKH---FLKRRVSKEALEALEEISEEFFEQLSDDLEAYADHAGRKTINEKDVEL 62
 
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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