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Conserved domains on  [gi|2085295306|ref|XP_043045373|]
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histone 3 [Guyanagaster necrorhizus MCA 3950]

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
 1-137 1.42e-75

histone H3; Provisional


:

Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 220.55  E-value: 1.42e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085295306   1 MARTKQTARKSTGGKAPRKQLATKAARKTAATAtGGVKKPHRFRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF 80
Cdd:PTZ00018    1 MARTKQTARKSTGGKAPRKQLASKAARKSAPVT-GGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2085295306  81 KTDLRFQSSAVMALQEAAEAYLVSLFEDTNLAAIHAKRVTIQPKDLALARRLRGERS 137
Cdd:PTZ00018   80 KTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERS 136
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-137 1.42e-75

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 220.55  E-value: 1.42e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085295306   1 MARTKQTARKSTGGKAPRKQLATKAARKTAATAtGGVKKPHRFRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF 80
Cdd:PTZ00018    1 MARTKQTARKSTGGKAPRKQLASKAARKSAPVT-GGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2085295306  81 KTDLRFQSSAVMALQEAAEAYLVSLFEDTNLAAIHAKRVTIQPKDLALARRLRGERS 137
Cdd:PTZ00018   80 KTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERS 136
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 41-134 7.63e-59

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: 176.96  E-value: 7.63e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085295306  41 HRFRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT-DLRFQSSAVMALQEAAEAYLVSLFEDTNLAAIHAKRV 119
Cdd:cd22911     1 RRYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTkDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRV 80

                          90
                  ....*....|....*
gi 2085295306 120 TIQPKDLALARRLRG 134
Cdd:cd22911    81 TLMPKDMQLARRIRG 95
H3 smart00428
Histone H3;
35-136 1.07e-55

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 169.17  E-value: 1.07e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085295306   35 GGVKKPHRFRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVMALQEAAEAYLVSLFEDTNLA 112
Cdd:smart00428   1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTgvDLRFQSSAIMALQEAAEAYLVGLFEDTNLL 80

                           90       100
                   ....*....|....*....|....
gi 2085295306  113 AIHAKRVTIQPKDLALARRLRGER 136
Cdd:smart00428  81 AIHAKRVTIMPKDIQLARRIRGER 104
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-133 4.03e-48

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 151.05  E-value: 4.03e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085295306   1 MARTKQTARKSTGGKAPRKQLATKAARKTAatatggvKKPHRFRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF 80
Cdd:pfam00125   1 MARNKNKANPRRGGTAPEKKISQKSSSSSK-------KKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQST 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2085295306  81 KTDLRFQSSAVMALQEAAEAYLVSLFEDTNLAAIHAKRVTIQPKDLALARRLR 133
Cdd:pfam00125  74 KTDLRISADAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 126
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
68-132 4.44e-03

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


Pssm-ID: 441639  Cd Length: 67  Bit Score: 33.65  E-value: 4.44e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2085295306  68 PFQRLVREIaqdfkTDLRFQSSAVMALQEAAEAYLVSLFEDTNLAAIHAKRVTIQPKDLALARRL 132
Cdd:COG2036     6 PVDRIIKKA-----GAERVSEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKL 65
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-137 1.42e-75

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 220.55  E-value: 1.42e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085295306   1 MARTKQTARKSTGGKAPRKQLATKAARKTAATAtGGVKKPHRFRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF 80
Cdd:PTZ00018    1 MARTKQTARKSTGGKAPRKQLASKAARKSAPVT-GGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2085295306  81 KTDLRFQSSAVMALQEAAEAYLVSLFEDTNLAAIHAKRVTIQPKDLALARRLRGERS 137
Cdd:PTZ00018   80 KTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERS 136
PLN00121 PLN00121
histone H3; Provisional
 1-137 2.94e-68

histone H3; Provisional


Pssm-ID: 177733 [Multi-domain]  Cd Length: 136  Bit Score: 202.21  E-value: 2.94e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085295306   1 MARTKQTARKSTGGKAPRKQLATKAARKTAATAtGGVKKPHRFRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF 80
Cdd:PLN00121    1 MARTKQTARKSTGGKAPRKQLATKAARKSAPAT-GGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDF 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2085295306  81 KTDLRFQSSAVMALQEAAEAYLVSLFEDTNLAAIHAKRVTIQPKDLALARRLRGERS 137
Cdd:PLN00121   80 KTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 136
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 41-134 7.63e-59

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: 176.96  E-value: 7.63e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085295306  41 HRFRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT-DLRFQSSAVMALQEAAEAYLVSLFEDTNLAAIHAKRV 119
Cdd:cd22911     1 RRYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTkDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRV 80

                          90
                  ....*....|....*
gi 2085295306 120 TIQPKDLALARRLRG 134
Cdd:cd22911    81 TLMPKDMQLARRIRG 95
H3 smart00428
Histone H3;
35-136 1.07e-55

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 169.17  E-value: 1.07e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085295306   35 GGVKKPHRFRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVMALQEAAEAYLVSLFEDTNLA 112
Cdd:smart00428   1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTgvDLRFQSSAIMALQEAAEAYLVGLFEDTNLL 80

                           90       100
                   ....*....|....*....|....
gi 2085295306  113 AIHAKRVTIQPKDLALARRLRGER 136
Cdd:smart00428  81 AIHAKRVTIMPKDIQLARRIRGER 104
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-133 4.03e-48

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 151.05  E-value: 4.03e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085295306   1 MARTKQTARKSTGGKAPRKQLATKAARKTAatatggvKKPHRFRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF 80
Cdd:pfam00125   1 MARNKNKANPRRGGTAPEKKISQKSSSSSK-------KKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQST 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2085295306  81 KTDLRFQSSAVMALQEAAEAYLVSLFEDTNLAAIHAKRVTIQPKDLALARRLR 133
Cdd:pfam00125  74 KTDLRISADAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 126
PLN00161 PLN00161
histone H3; Provisional
 1-134 4.42e-42

histone H3; Provisional


Pssm-ID: 215082 [Multi-domain]  Cd Length: 135  Bit Score: 135.90  E-value: 4.42e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085295306   1 MARTKQtARKSTGGKAPRKQLATKAARKTAatatggvKKPHRFRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF 80
Cdd:PLN00161    1 MARRLQ-GKRFRKGKKPQKEASGVTRQELD-------KKPHRYRPGTVALREIRKYQKSTELLIRKLPFARLVREISNEM 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2085295306  81 KTD-LRFQSSAVMALQEAAEAYLVSLFEDTNLAAIHAKRVTIQPKDLALARRLRG 134
Cdd:PLN00161   73 LREpFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRIRG 127
PLN00160 PLN00160
histone H3; Provisional
 44-135 1.63e-34

histone H3; Provisional


Pssm-ID: 165727  Cd Length: 97  Bit Score: 115.53  E-value: 1.63e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2085295306  44 RPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF-KTDLRFQSSAVMALQEAAEAYLVSLFEDTNLAAIHAKRVTIQ 122
Cdd:PLN00160    2 RPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMsREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIM 81

                          90
                  ....*....|...
gi 2085295306 123 PKDLALARRLRGE 135
Cdd:PLN00160   82 PKDMQLARRIRGQ 94
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 69-129 2.56e-05

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: 39.51  E-value: 2.56e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2085295306  69 FQRLVREIAQDFKTDlRFQSSAVMALQEAAEAYLVSLFEDTNLAAIHAKRVTIQPKDLALA 129
Cdd:cd00076     2 LRSAVARILKSAGFD-SVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELA 61
HFD_CENP-T cd22920
histone-fold domain found in centromere protein T (CENP-T) and similar proteins; CENP-T, also ...
 71-133 5.23e-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: 36.76  E-value: 5.23e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2085295306  71 RLVREIAQdFKTDLRFQSSAVMALQEAAEAYLVSLFEDTNLAAIHAKRVTIQPKD-LALARRLR 133
Cdd:cd22920     6 SLVKKLFK-HFLKRRVSKEALEALEEISEEFFEQLSDDLEAYADHAGRKTINEKDvELLMKRQR 68
CENP-S pfam15630
CENP-S protein; CENP-S is a family of vertebral and fungal kinetochore component proteins. ...
 70-131 2.02e-03

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: 34.86  E-value: 2.02e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2085295306  70 QRLVREIAQDFKTDlrFQSSAVMALQEAAEAYLVSLFEDTNLAAIHAKRVTIQPKD-LALARR 131
Cdd:pfam15630  12 GKIVEEETLDLGVN--ATPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTITTDDvKLLARR 72
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
68-132 4.44e-03

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


Pssm-ID: 441639  Cd Length: 67  Bit Score: 33.65  E-value: 4.44e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2085295306  68 PFQRLVREIaqdfkTDLRFQSSAVMALQEAAEAYLVSLFEDTNLAAIHAKRVTIQPKDLALARRL 132
Cdd:COG2036     6 PVDRIIKKA-----GAERVSEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKL 65
HFD_CENP-S cd22919
histone-fold domain found in centromere protein S (CENP-S) and similar proteins; CENP-S, also ...
 71-131 4.50e-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: 34.08  E-value: 4.50e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2085295306  71 RLVREIAQdfKTDLRFQSSAVMALQEAAEAYLVSLFEDTNLAAIHAKRVTIQPKDLAL-ARR 131
Cdd:cd22919    11 KICEEEAE--EKGVTVSPQFVAALAELVYKQLESLARDLEAFARHAKRKTITVDDVKLlARR 70
 
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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