NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1928915568|ref|NP_001157888|]
View 

histone H2B type F-M [Homo sapiens]

Protein Classification

histone H2B family protein( domain architecture ID 581091)

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
SCOP:  4000793

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 53-137 3.92e-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: 137.65  E-value: 3.92e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928915568  53 SFTPYFPRVLKQVHQGLSLSQEAVSVMDSMIHDILDRIATEAGQLAHYTKRVTITSRDIQMAVRLLLPGKMGKLAEAQGT 132
Cdd:cd22910     8 SFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVSEGT 87


                  ....*
gi 1928915568 133 NAALR 137
Cdd:cd22910    88 KAVTK 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 ...
 53-137 3.92e-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: 137.65  E-value: 3.92e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928915568  53 SFTPYFPRVLKQVHQGLSLSQEAVSVMDSMIHDILDRIATEAGQLAHYTKRVTITSRDIQMAVRLLLPGKMGKLAEAQGT 132
Cdd:cd22910     8 SFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVSEGT 87


                  ....*
gi 1928915568 133 NAALR 137
Cdd:cd22910    88 KAVTK 92
PLN00158 PLN00158
histone H2B; Provisional
 52-139 3.37e-27

histone H2B; Provisional


Pssm-ID: 215081  Cd Length: 116  Bit Score: 97.84  E-value: 3.37e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928915568  52 DSFTPYFPRVLKQVHQGLSLSQEAVSVMDSMIHDILDRIATEAGQLAHYTKRVTITSRDIQMAVRLLLPGKMGKLAEAQG 131
Cdd:PLN00158   27 ETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLILPGELAKHAVSEG 106


                  ....*...
gi 1928915568 132 TNAALRTS 139
Cdd:PLN00158  107 TKAVTKFT 114
H2B smart00427
Histone H2B;
52-139 9.67e-27

Histone H2B;


Pssm-ID: 197718  Cd Length: 97  Bit Score: 96.05  E-value: 9.67e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928915568   52 DSFTPYFPRVLKQVHQGLSLSQEAVSVMDSMIHDILDRIATEAGQLAHYTKRVTITSRDIQMAVRLLLPGKMGKLAEAQG 131
Cdd:smart00427   9 ETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVSEG 88


                   ....*...
gi 1928915568  132 TNAALRTS 139
Cdd:smart00427  89 TKAVTKAS 96
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-118 8.55e-20

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 79.01  E-value: 8.55e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928915568   1 MAEASSETTSEEGQSIQEPkEANSTKAQKQKRRGCRGSRRRHANRRGDSFgDSFTPYFPRVLKQVHQ----GLSLSQEAV 76
Cdd:pfam00125   7 KANPRRGGTAPEKKISQKS-SSSSKKKTRRYRPGTVALKEIRKYQSSTDL-LIYKLPFARVVREVVQstktDLRISADAV 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1928915568  77 SVMDSMIHDILDRIATEAGQLAHYTKRVTITSRDIQMAVRLL 118
Cdd:pfam00125  85 VALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 126
 
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 ...
 53-137 3.92e-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: 137.65  E-value: 3.92e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928915568  53 SFTPYFPRVLKQVHQGLSLSQEAVSVMDSMIHDILDRIATEAGQLAHYTKRVTITSRDIQMAVRLLLPGKMGKLAEAQGT 132
Cdd:cd22910     8 SFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVSEGT 87


                  ....*
gi 1928915568 133 NAALR 137
Cdd:cd22910    88 KAVTK 92
PLN00158 PLN00158
histone H2B; Provisional
 52-139 3.37e-27

histone H2B; Provisional


Pssm-ID: 215081  Cd Length: 116  Bit Score: 97.84  E-value: 3.37e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928915568  52 DSFTPYFPRVLKQVHQGLSLSQEAVSVMDSMIHDILDRIATEAGQLAHYTKRVTITSRDIQMAVRLLLPGKMGKLAEAQG 131
Cdd:PLN00158   27 ETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLILPGELAKHAVSEG 106


                  ....*...
gi 1928915568 132 TNAALRTS 139
Cdd:PLN00158  107 TKAVTKFT 114
H2B smart00427
Histone H2B;
52-139 9.67e-27

Histone H2B;


Pssm-ID: 197718  Cd Length: 97  Bit Score: 96.05  E-value: 9.67e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928915568   52 DSFTPYFPRVLKQVHQGLSLSQEAVSVMDSMIHDILDRIATEAGQLAHYTKRVTITSRDIQMAVRLLLPGKMGKLAEAQG 131
Cdd:smart00427   9 ETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVSEG 88


                   ....*...
gi 1928915568  132 TNAALRTS 139
Cdd:smart00427  89 TKAVTKAS 96
PTZ00463 PTZ00463
histone H2B; Provisional
 45-137 6.64e-20

histone H2B; Provisional


Pssm-ID: 185642  Cd Length: 117  Bit Score: 79.45  E-value: 6.64e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928915568  45 RRGDSFGDSFTPYFPRVLKQVHQGLSLSQEAVSVMDSMIHDILDRIATEAGQLAHYTKRVTITSRDIQMAVRLLLPGKMG 124
Cdd:PTZ00463   21 KRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLVLPGELA 100

                          90
                  ....*....|...
gi 1928915568 125 KLAEAQGTNAALR 137
Cdd:PTZ00463  101 KHAVSEGTKAVTK 113
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-118 8.55e-20

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 79.01  E-value: 8.55e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928915568   1 MAEASSETTSEEGQSIQEPkEANSTKAQKQKRRGCRGSRRRHANRRGDSFgDSFTPYFPRVLKQVHQ----GLSLSQEAV 76
Cdd:pfam00125   7 KANPRRGGTAPEKKISQKS-SSSSKKKTRRYRPGTVALKEIRKYQSSTDL-LIYKLPFARVVREVVQstktDLRISADAV 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1928915568  77 SVMDSMIHDILDRIATEAGQLAHYTKRVTITSRDIQMAVRLL 118
Cdd:pfam00125  85 VALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 126
HFD_archaea_histone-like cd22909
histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription ...
 60-116 5.54e-05

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: 39.06  E-value: 5.54e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1928915568  60 RVLKQVHqGLSLSQEAVSVMDSMIHDILDRIATEAGQLAHYTKRVTITSRDIQMAVR 116
Cdd:cd22909     9 RIIKKAG-AERVSEDAAEELAKLLEEIAEEIAEEAVKLAKHAGRKTVKAEDIELAVK 64
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 60-116 9.03e-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: 38.35  E-value: 9.03e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1928915568  60 RVLKQVHqGLSLSQEAVSVMDSMIHDILDRIATEAGQLAHYTKRVTITSRDIQMAVR 116
Cdd:cd00076     8 RILKSAG-FDSVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELALE 63
HFD_TAF12 cd07981
histone-fold domain found in transcription initiation factor TFIID subunit 12 (TAF12) and ...
 62-116 2.00e-04

histone-fold domain found in transcription initiation factor TFIID subunit 12 (TAF12) and similar proteins; TAF12, also called TATA Binding Protein (TBP) associated factor 12, transcription initiation factor TFIID 20/15 kDa subunits, TAFII-20/TAFII-15, or TAFII20/TAFII15, is a TBP-associated factor (TAF). TAFs are components of the transcription factor IID (TFIID) complex, PCAF histone acetylase complex, and TBP-free TAFII complex (TFTC). TIIFD is multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. TFIID and PCAF are composed of TATA binding protein (TBP) and several TAFs. TBP is not part of TFTC. TAFs are essential for mediating regulation of RNA polymerase transcription. TAF12 interacts with TAF4 and makes a novel histone-like heterodimer that binds DNA and has a core promoter function of a subset of genes. It is important for RAS-induced transformation properties of human colorectal cancer cells; its levels are increased in the cells harboring the RAS mutation. Also, TAF12 interacts with activating transcription factor 7 (ATF7) and contributes to the hypersensitivity of osteoclast (OCL) precursors to 1,25-dihydroxyvitamin D2 (1,25-(OH)2D3; also known as calcitriol) in Paget's disease (PD), a disorder of the bone remodeling process, in which the body absorbs old bone and forms abnormal new bone.


Pssm-ID: 467025 [Multi-domain]  Cd Length: 74  Bit Score: 37.51  E-value: 2.00e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1928915568  62 LKQVHQGLSLSQEAVSVMDSMIHDILDRIATEAGQLAHYTKRVTITSRDIQMAVR 116
Cdd:cd07981    13 VREVDPNERLDPDVEELLLQLADDFVDDVVTFACKLAKHRGSDTLEVKDVQLHLE 67
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH