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Conserved domains on  [gi|1928577664|ref|NP_001002916|]
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histone H2B type W-T [Homo sapiens]

Protein Classification

histone H2B family protein( domain architecture ID 19223400)

histone H2B is one of 4 core histone proteins, H2A, H2B, H3 and H4 to form the nucleosome core particle

CATH:  1.10.20.10
Gene Ontology:  GO:0003677|GO:0005634|GO:0000786|GO:0046982|GO:0044877|GO:0030527

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HFD_H2B cd22910
histone-fold domain found in histone H2B and similar proteins; Histone H2B is a core component ...
 49-136 2.11e-43

histone-fold domain found in histone H2B and similar proteins; Histone H2B 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. Some histone H2B family members have broad antibacterial activity, which may contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.


:

Pssm-ID: 467035  Cd Length: 94  Bit Score: 138.03  E-value: 2.11e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928577664  49 RGDSFATYFRRVLKQVHQGLSLSREAVSVMDSLVHDILDRIATEAGHLARSTKRQTITAWETRMAVRLLLPGQMGKLAES 128
Cdd:cd22910     5 RKESFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVS 84


                  ....*...
gi 1928577664 129 EGTKAVLR 136
Cdd:cd22910    85 EGTKAVTK 92
 
Name Accession Description Interval E-value
HFD_H2B cd22910
histone-fold domain found in histone H2B and similar proteins; Histone H2B is a core component ...
 49-136 2.11e-43

histone-fold domain found in histone H2B and similar proteins; Histone H2B 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. Some histone H2B family members have broad antibacterial activity, which may contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.


Pssm-ID: 467035  Cd Length: 94  Bit Score: 138.03  E-value: 2.11e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928577664  49 RGDSFATYFRRVLKQVHQGLSLSREAVSVMDSLVHDILDRIATEAGHLARSTKRQTITAWETRMAVRLLLPGQMGKLAES 128
Cdd:cd22910     5 RKESFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVS 84


                  ....*...
gi 1928577664 129 EGTKAVLR 136
Cdd:cd22910    85 EGTKAVTK 92
PLN00158 PLN00158
histone H2B; Provisional
 25-138 1.86e-29

histone H2B; Provisional


Pssm-ID: 215081  Cd Length: 116  Bit Score: 103.62  E-value: 1.86e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928577664  25 TTSQKQSKQRKRGRHGPRRchsNCRGDSFATYFRRVLKQVHQGLSLSREAVSVMDSLVHDILDRIATEAGHLARSTKRQT 104
Cdd:PLN00158    4 TPSKKPAKKAAKGAKKKGS---KSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPT 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1928577664 105 ITAWETRMAVRLLLPGQMGKLAESEGTKAVLRTS 138
Cdd:PLN00158   81 VTSREIQTAVRLILPGELAKHAVSEGTKAVTKFT 114
H2B smart00427
Histone H2B;
49-138 2.89e-27

Histone H2B;


Pssm-ID: 197718  Cd Length: 97  Bit Score: 97.59  E-value: 2.89e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928577664   49 RGDSFATYFRRVLKQVHQGLSLSREAVSVMDSLVHDILDRIATEAGHLARSTKRQTITAWETRMAVRLLLPGQMGKLAES 128
Cdd:smart00427   7 RKETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVS 86

                           90
                   ....*....|
gi 1928577664  129 EGTKAVLRTS 138
Cdd:smart00427  87 EGTKAVTKAS 96
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-117 4.50e-25

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 92.50  E-value: 4.50e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928577664   1 MAGPSSETTSEEQLITQEPkEANSTTSQKQSKQRKRGRHGPRRCHSNCRGDSFATYFRRVLKQVHQ----GLSLSREAVS 76
Cdd:pfam00125   7 KANPRRGGTAPEKKISQKS-SSSSKKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQstktDLRISADAVV 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1928577664  77 VMDSLVHDILDRIATEAGHLARSTKRQTITAWETRMAVRLL 117
Cdd:pfam00125  86 ALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 126
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
71-117 8.04e-03

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


Pssm-ID: 441639  Cd Length: 67  Bit Score: 33.27  E-value: 8.04e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1928577664  71 SREAVSVMDSLVHDILDRIATEAGHLARSTKRQTITAWETRMAVRLL 117
Cdd:COG2036    20 SEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKLL 66
 
Name Accession Description Interval E-value
HFD_H2B cd22910
histone-fold domain found in histone H2B and similar proteins; Histone H2B is a core component ...
 49-136 2.11e-43

histone-fold domain found in histone H2B and similar proteins; Histone H2B 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. Some histone H2B family members have broad antibacterial activity, which may contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.


Pssm-ID: 467035  Cd Length: 94  Bit Score: 138.03  E-value: 2.11e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928577664  49 RGDSFATYFRRVLKQVHQGLSLSREAVSVMDSLVHDILDRIATEAGHLARSTKRQTITAWETRMAVRLLLPGQMGKLAES 128
Cdd:cd22910     5 RKESFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVS 84


                  ....*...
gi 1928577664 129 EGTKAVLR 136
Cdd:cd22910    85 EGTKAVTK 92
PLN00158 PLN00158
histone H2B; Provisional
 25-138 1.86e-29

histone H2B; Provisional


Pssm-ID: 215081  Cd Length: 116  Bit Score: 103.62  E-value: 1.86e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928577664  25 TTSQKQSKQRKRGRHGPRRchsNCRGDSFATYFRRVLKQVHQGLSLSREAVSVMDSLVHDILDRIATEAGHLARSTKRQT 104
Cdd:PLN00158    4 TPSKKPAKKAAKGAKKKGS---KSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPT 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1928577664 105 ITAWETRMAVRLLLPGQMGKLAESEGTKAVLRTS 138
Cdd:PLN00158   81 VTSREIQTAVRLILPGELAKHAVSEGTKAVTKFT 114
H2B smart00427
Histone H2B;
49-138 2.89e-27

Histone H2B;


Pssm-ID: 197718  Cd Length: 97  Bit Score: 97.59  E-value: 2.89e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928577664   49 RGDSFATYFRRVLKQVHQGLSLSREAVSVMDSLVHDILDRIATEAGHLARSTKRQTITAWETRMAVRLLLPGQMGKLAES 128
Cdd:smart00427   7 RKETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVS 86

                           90
                   ....*....|
gi 1928577664  129 EGTKAVLRTS 138
Cdd:smart00427  87 EGTKAVTKAS 96
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-117 4.50e-25

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 92.50  E-value: 4.50e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928577664   1 MAGPSSETTSEEQLITQEPkEANSTTSQKQSKQRKRGRHGPRRCHSNCRGDSFATYFRRVLKQVHQ----GLSLSREAVS 76
Cdd:pfam00125   7 KANPRRGGTAPEKKISQKS-SSSSKKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQstktDLRISADAVV 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1928577664  77 VMDSLVHDILDRIATEAGHLARSTKRQTITAWETRMAVRLL 117
Cdd:pfam00125  86 ALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 126
PTZ00463 PTZ00463
histone H2B; Provisional
 14-136 6.18e-21

histone H2B; Provisional


Pssm-ID: 185642  Cd Length: 117  Bit Score: 81.76  E-value: 6.18e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928577664  14 LITQEPKEAN-STTSQKQSKQRKRGRHgprrchsncrgDSFATYFRRVLKQVHQGLSLSREAVSVMDSLVHDILDRIATE 92
Cdd:PTZ00463    1 MVSKKPAKAKkAATGPDGKKKRKKSRY-----------DSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATE 69

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1928577664  93 AGHLARSTKRQTITAWETRMAVRLLLPGQMGKLAESEGTKAVLR 136
Cdd:PTZ00463   70 ASRLCKYTRRDTLSSREIQTAIRLVLPGELAKHAVSEGTKAVTK 113
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 58-115 6.93e-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: 36.04  E-value: 6.93e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1928577664  58 RRVLKQVHqGLSLSREAVSVMDSLVHDILDRIATEAGHLARSTKRQTITAWETRMAVR 115
Cdd:cd00076     7 ARILKSAG-FDSVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELALE 63
HFD_archaea_histone-like cd22909
histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription ...
 57-115 2.11e-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: 34.83  E-value: 2.11e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1928577664  57 FRRVLKQVHqGLSLSREAVSVMDSLVHDILDRIATEAGHLARSTKRQTITAWETRMAVR 115
Cdd:cd22909     7 VKRIIKKAG-AERVSEDAAEELAKLLEEIAEEIAEEAVKLAKHAGRKTVKAEDIELAVK 64
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
71-117 8.04e-03

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


Pssm-ID: 441639  Cd Length: 67  Bit Score: 33.27  E-value: 8.04e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1928577664  71 SREAVSVMDSLVHDILDRIATEAGHLARSTKRQTITAWETRMAVRLL 117
Cdd:COG2036    20 SEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKLL 66
 
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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