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Conserved domains on  [gi|157277186|gb|ABV29086|]
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histone H3, partial [Cladosporium aff. cladosporioides CPC 11606]

Protein Classification

histone H3( domain architecture ID 10794185)

histone H3 is a core component of the nucleosome that wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template

CATH:  1.10.20.10
Gene Ontology:  GO:0003677|GO:0046982|GO:0030527
PubMed:  8121801|33155135

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-122 5.18e-77

histone H3; Provisional


:

Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 223.63  E-value: 5.18e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157277186   1 RSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKSDLRFQSSA 80
Cdd:PTZ00018  10 KSTGGKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSA 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 157277186  81 IGALQESVEAYLVSLFEDTNLCAIHAKRVTIQSKDIQLARRL 122
Cdd:PTZ00018  90 VLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-122 5.18e-77

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 223.63  E-value: 5.18e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157277186   1 RSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKSDLRFQSSA 80
Cdd:PTZ00018  10 KSTGGKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSA 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 157277186  81 IGALQESVEAYLVSLFEDTNLCAIHAKRVTIQSKDIQLARRL 122
Cdd:PTZ00018  90 VLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 31-122 2.62e-60

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: 180.04  E-value: 2.62e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157277186  31 HRYKPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK-SDLRFQSSAIGALQESVEAYLVSLFEDTNLCAIHAKRV 109
Cdd:cd22911    1 RRYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKtKDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRV 80

                         90
                 ....*....|...
gi 157277186 110 TIQSKDIQLARRL 122
Cdd:cd22911   81 TLMPKDMQLARRI 93
H3 smart00428
Histone H3;
25-122 2.02e-54

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 165.31  E-value: 2.02e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157277186    25 GGVKKPHRYKPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK--SDLRFQSSAIGALQESVEAYLVSLFEDTNLC 102
Cdd:smart00428   1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTtgVDLRFQSSAIMALQEAAEAYLVGLFEDTNLL 80

                           90       100
                   ....*....|....*....|
gi 157277186   103 AIHAKRVTIQSKDIQLARRL 122
Cdd:smart00428  81 AIHAKRVTIMPKDIQLARRI 100
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-122 4.73e-47

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 147.58  E-value: 4.73e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157277186    1 RSTGGKAPRKQLASKAARKSapstggVKKPHRYKPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKSDLRFQSSA 80
Cdd:pfam00125  10 PRRGGTAPEKKISQKSSSSS------KKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQSTKTDLRISADA 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 157277186   81 IGALQESVEAYLVSLFEDTNLCAIHAKRVTIQSKDIQLARRL 122
Cdd:pfam00125  84 VVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRL 125
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
58-122 4.95e-03

Archaeal histone H3/H4 [Chromatin structure and dynamics];


Pssm-ID: 441639  Cd Length: 67  Bit Score: 33.27  E-value: 4.95e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157277186  58 PFQRLVREIAqdfksDLRFQSSAIGALQESVEAYLVSLFEDTNLCAIHAKRVTIQSKDIQLARRL 122
Cdd:COG2036    6 PVDRIIKKAG-----AERVSEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKL 65
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-122 5.18e-77

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 223.63  E-value: 5.18e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157277186   1 RSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKSDLRFQSSA 80
Cdd:PTZ00018  10 KSTGGKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSA 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 157277186  81 IGALQESVEAYLVSLFEDTNLCAIHAKRVTIQSKDIQLARRL 122
Cdd:PTZ00018  90 VLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131
PLN00121 PLN00121
histone H3; Provisional
 1-122 6.82e-70

histone H3; Provisional


Pssm-ID: 177733 [Multi-domain]  Cd Length: 136  Bit Score: 205.67  E-value: 6.82e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157277186   1 RSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKSDLRFQSSA 80
Cdd:PLN00121  10 KSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSA 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 157277186  81 IGALQESVEAYLVSLFEDTNLCAIHAKRVTIQSKDIQLARRL 122
Cdd:PLN00121  90 VLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 31-122 2.62e-60

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: 180.04  E-value: 2.62e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157277186  31 HRYKPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK-SDLRFQSSAIGALQESVEAYLVSLFEDTNLCAIHAKRV 109
Cdd:cd22911    1 RRYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKtKDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRV 80

                         90
                 ....*....|...
gi 157277186 110 TIQSKDIQLARRL 122
Cdd:cd22911   81 TLMPKDMQLARRI 93
H3 smart00428
Histone H3;
25-122 2.02e-54

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 165.31  E-value: 2.02e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157277186    25 GGVKKPHRYKPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK--SDLRFQSSAIGALQESVEAYLVSLFEDTNLC 102
Cdd:smart00428   1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTtgVDLRFQSSAIMALQEAAEAYLVGLFEDTNLL 80

                           90       100
                   ....*....|....*....|
gi 157277186   103 AIHAKRVTIQSKDIQLARRL 122
Cdd:smart00428  81 AIHAKRVTIMPKDIQLARRI 100
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-122 4.73e-47

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 147.58  E-value: 4.73e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157277186    1 RSTGGKAPRKQLASKAARKSapstggVKKPHRYKPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKSDLRFQSSA 80
Cdd:pfam00125  10 PRRGGTAPEKKISQKSSSSS------KKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQSTKTDLRISADA 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 157277186   81 IGALQESVEAYLVSLFEDTNLCAIHAKRVTIQSKDIQLARRL 122
Cdd:pfam00125  84 VVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRL 125
PLN00161 PLN00161
histone H3; Provisional
 1-122 1.52e-41

histone H3; Provisional


Pssm-ID: 215082 [Multi-domain]  Cd Length: 135  Bit Score: 133.97  E-value: 1.52e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157277186   1 RSTGGKAPRKqlASKAARKSAPSTGGV--KKPHRYKPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKSD-LRFQ 77
Cdd:PLN00161   3 RRLQGKRFRK--GKKPQKEASGVTRQEldKKPHRYRPGTVALREIRKYQKSTELLIRKLPFARLVREISNEMLREpFRWT 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 157277186  78 SSAIGALQESVEAYLVSLFEDTNLCAIHAKRVTIQSKDIQLARRL 122
Cdd:PLN00161  81 AEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRI 125
PLN00160 PLN00160
histone H3; Provisional
 34-122 3.37e-34

histone H3; Provisional


Pssm-ID: 165727  Cd Length: 97  Bit Score: 113.99  E-value: 3.37e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157277186  34 KPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF-KSDLRFQSSAIGALQESVEAYLVSLFEDTNLCAIHAKRVTIQ 112
Cdd:PLN00160   2 RPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMsREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIM 81

                         90
                 ....*....|
gi 157277186 113 SKDIQLARRL 122
Cdd:PLN00160  82 PKDMQLARRI 91
CENP-S pfam15630
CENP-S protein; CENP-S is a family of vertebral and fungal kinetochore component proteins. ...
 60-121 1.08e-04

CENP-S protein; CENP-S is a family of vertebral and fungal kinetochore component proteins. CENP-S complexes with CENP-X to form a stable CENP-T-W-S-X heterotetramer.


Pssm-ID: 464782  Cd Length: 76  Bit Score: 37.94  E-value: 1.08e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 157277186   60 QRLVREIAQDFksDLRFQSSAIGALQESVEAYLVSLFEDTNLCAIHAKRVTIQSKDIQL-ARR 121
Cdd:pfam15630  12 GKIVEEETLDL--GVNATPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTITTDDVKLlARR 72
HFD_CENP-T cd22920
histone-fold domain found in centromere protein T (CENP-T) and similar proteins; CENP-T, also ...
 61-118 5.74e-04

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: 36.38  E-value: 5.74e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 157277186  61 RLVREIAQdFKSDLRFQSSAIGALQESVEAYLVSLFEDTNLCAIHAKRVTIQSKDIQL 118
Cdd:cd22920    6 SLVKKLFK-HFLKRRVSKEALEALEEISEEFFEQLSDDLEAYADHAGRKTINEKDVEL 62
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 59-119 1.12e-03

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: 34.89  E-value: 1.12e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 157277186  59 FQRLVREIAQDFkSDLRFQSSAIGALQESVEAYLVSLFEDTNLCAIHAKRVTIQSKDIQLA 119
Cdd:cd00076    2 LRSAVARILKSA-GFDSVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELA 61
HFD_CENP-S cd22919
histone-fold domain found in centromere protein S (CENP-S) and similar proteins; CENP-S, also ...
 61-121 1.33e-03

histone-fold domain found in centromere protein S (CENP-S) and similar proteins; CENP-S, also called MHF1, apoptosis-inducing TAF9-like domain-containing protein 1 (APITD1), FANCM-associated histone fold protein 1, FANCM-interacting histone fold protein 1, or Fanconi anemia-associated polypeptide of 16 kDa (FAAP16), is a DNA-binding component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. CENP-S, together with CENP-X, forms the MHF heterodimer, which can further assemble to form tetrameric structures. CENP-S acts as a crucial cofactor for FANCM, in both binding and ATP-dependent remodeling of DNA. It can stabilize FANCM. CENP-S also forms a discrete complex with FANCM and CENP-X, called FANCM-MHF. This interaction leads to synergistic activation of double-stranded DNA binding and strongly stimulates FANCM-mediated DNA remodeling. In complex with CENP-T, CENP-W and CENP-X (CENP-T-W-S-X heterotetramer), CENP-S is involved in the formation of a functional kinetochore outer plate, which is essential for kinetochore-microtubule attachment and faithful mitotic progression. As a component of MHF and CENP-T-W-S-X complexes, CENP-S binds DNA and bends it to form a nucleosome-like structure. Its DNA-binding function is fulfilled in the presence of CENP-X. It does not bind DNA on its own.


Pssm-ID: 467044  Cd Length: 77  Bit Score: 35.23  E-value: 1.33e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 157277186  61 RLVREIAQdfKSDLRFQSSAIGALQESVEAYLVSLFEDTNLCAIHAKRVTIQSKDIQL-ARR 121
Cdd:cd22919   11 KICEEEAE--EKGVTVSPQFVAALAELVYKQLESLARDLEAFARHAKRKTITVDDVKLlARR 70
HFD_archaea_histone-like cd22909
histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription ...
 56-121 4.85e-03

histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription regulators and similar proteins; The family includes many archaeal histone-fold proteins and histone-like transcription regulators, which may bind and compact DNA (95 to 150 base pairs) to form nucleosome-like structures that contain positive DNA supercoils. They can increase the resistance of DNA to thermal denaturation.


Pssm-ID: 467034  Cd Length: 64  Bit Score: 33.29  E-value: 4.85e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157277186  56 KLPFQRLVREIaqdfkSDLRFQSSAIGALQESVEAYLVSLFEDTNLCAIHAKRVTIQSKDIQLARR 121
Cdd:cd22909    4 KAPVKRIIKKA-----GAERVSEDAAEELAKLLEEIAEEIAEEAVKLAKHAGRKTVKAEDIELAVK 64
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
58-122 4.95e-03

Archaeal histone H3/H4 [Chromatin structure and dynamics];


Pssm-ID: 441639  Cd Length: 67  Bit Score: 33.27  E-value: 4.95e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157277186  58 PFQRLVREIAqdfksDLRFQSSAIGALQESVEAYLVSLFEDTNLCAIHAKRVTIQSKDIQLARRL 122
Cdd:COG2036    6 PVDRIIKKAG-----AERVSEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKL 65
 
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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