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Protein

Histone H2B type 1-H

Gene

HIST1H2BH

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Core component of nucleosome. Nucleosomes wrap and compact 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 histone code, and nucleosome remodeling.

GO - Molecular functioni

  • DNA binding Source: UniProtKB

GO - Biological processi

  • nucleosome assembly Source: UniProtKB
Complete GO annotation...

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiR-HSA-1221632. Meiotic synapsis.
R-HSA-171306. Packaging Of Telomere Ends.
R-HSA-201722. Formation of the beta-catenin:TCF transactivating complex.
R-HSA-212300. PRC2 methylates histones and DNA.
R-HSA-2299718. Condensation of Prophase Chromosomes.
R-HSA-2559580. Oxidative Stress Induced Senescence.
R-HSA-2559582. Senescence-Associated Secretory Phenotype (SASP).
R-HSA-2559586. DNA Damage/Telomere Stress Induced Senescence.
R-HSA-3214815. HDACs deacetylate histones.
R-HSA-3214847. HATs acetylate histones.
R-HSA-427359. SIRT1 negatively regulates rRNA Expression.
R-HSA-427389. ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression.
R-HSA-427413. NoRC negatively regulates rRNA expression.
R-HSA-5250924. B-WICH complex positively regulates rRNA expression.
R-HSA-5334118. DNA methylation.
R-HSA-5578749. Transcriptional regulation by small RNAs.
R-HSA-5617472. Activation of anterior HOX genes in hindbrain development during early embryogenesis.
R-HSA-5625886. Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3.
R-HSA-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
R-HSA-5693571. Nonhomologous End-Joining (NHEJ).
R-HSA-5693607. Processing of DNA double-strand break ends.
R-HSA-606279. Deposition of new CENPA-containing nucleosomes at the centromere.
R-HSA-69473. G2/M DNA damage checkpoint.
R-HSA-73728. RNA Polymerase I Promoter Opening.
R-HSA-73777. RNA Polymerase I Chain Elongation.
R-HSA-912446. Meiotic recombination.
R-HSA-977225. Amyloid fiber formation.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H2B type 1-H
Alternative name(s):
Histone H2B.j
Short name:
H2B/j
Gene namesi
Name:HIST1H2BH
Synonyms:H2BFJ
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

HGNCiHGNC:4755. HIST1H2BH.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: HPA
  • extracellular exosome Source: UniProtKB
  • nuclear nucleosome Source: GO_Central
  • nucleoplasm Source: HPA
  • nucleosome Source: UniProtKB
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA29130.

Polymorphism and mutation databases

BioMutaiHIST1H2BH.
DMDMi7387739.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 126125Histone H2B type 1-HPRO_0000071833Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylprolineBy similarity
Modified residuei6 – 61N6-acetyllysine; alternate2 Publications
Modified residuei6 – 61N6-crotonyllysine; alternate1 Publication
Cross-linki6 – 6Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateBy similarity
Modified residuei12 – 121N6-acetyllysine; alternate1 Publication
Modified residuei12 – 121N6-crotonyllysine; alternate1 Publication
Modified residuei13 – 131N6-acetyllysine; alternate2 Publications
Modified residuei13 – 131N6-crotonyllysine; alternate1 Publication
Modified residuei15 – 151Phosphoserine; by STK4/MST11 Publication
Modified residuei16 – 161N6-acetyllysine; alternate2 Publications
Modified residuei16 – 161N6-crotonyllysine; alternate1 Publication
Modified residuei17 – 171N6-acetyllysine; alternate1 Publication
Modified residuei17 – 171N6-crotonyllysine; alternate1 Publication
Modified residuei21 – 211N6-acetyllysine; alternate2 Publications
Modified residuei21 – 211N6-crotonyllysine; alternate1 Publication
Modified residuei24 – 241N6-acetyllysine; alternateBy similarity
Modified residuei24 – 241N6-crotonyllysine; alternate1 Publication
Modified residuei35 – 351N6-crotonyllysine; alternate1 Publication
Cross-linki35 – 35Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate1 Publication
Modified residuei37 – 371Phosphoserine; by AMPKBy similarity
Modified residuei47 – 471N6-methyllysine1 Publication
Modified residuei58 – 581N6,N6-dimethyllysine1 Publication
Modified residuei80 – 801Dimethylated arginineBy similarity
Modified residuei86 – 861N6,N6,N6-trimethyllysine; alternateBy similarity
Modified residuei86 – 861N6-acetyllysine; alternateBy similarity
Modified residuei87 – 871Omega-N-methylarginineBy similarity
Modified residuei93 – 931Omega-N-methylarginineBy similarity
Modified residuei109 – 1091N6-methyllysine1 Publication
Glycosylationi113 – 1131O-linked (GlcNAc)By similarity
Modified residuei116 – 1161PhosphothreonineBy similarity
Modified residuei117 – 1171N6-methylated lysineBy similarity
Cross-linki121 – 121Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)3 Publications

Post-translational modificationi

Monoubiquitination at Lys-35 (H2BK34Ub) by the MSL1/MSL2 dimer is required for histone H3 'Lys-4' (H3K4me) and 'Lys-79' (H3K79me) methylation and transcription activation at specific gene loci, such as HOXA9 and MEIS1 loci. Similarly, monoubiquitination at Lys-121 (H2BK120Ub) by the RNF20/40 complex gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation. It also functions cooperatively with the FACT dimer to stimulate elongation by RNA polymerase II. H2BK120Ub also acts as a regulator of mRNA splicing: deubiquitination by USP49 is required for efficient cotranscriptional splicing of a large set of exons.1 Publication
Phosphorylation at Ser-37 (H2BS36ph) by AMPK in response to stress promotes transcription (By similarity). Phosphorylated on Ser-15 (H2BS14ph) by STK4/MST1 during apoptosis; which facilitates apoptotic chromatin condensation. Also phosphorylated on Ser-15 in response to DNA double strand breaks (DSBs), and in correlation with somatic hypermutation and immunoglobulin class-switch recombination.By similarity1 Publication
GlcNAcylation at Ser-113 promotes monoubiquitination of Lys-121. It fluctuates in response to extracellular glucose, and associates with transcribed genes (By similarity).By similarity
Crotonylation (Kcr) is specifically present in male germ cells and marks testis-specific genes in post-meiotic cells, including X-linked genes that escape sex chromosome inactivation in haploid cells. Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors. It is also associated with post-meiotically activated genes on autosomes.1 Publication

Keywords - PTMi

Acetylation, Glycoprotein, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ93079.
MaxQBiQ93079.
PaxDbiQ93079.
PeptideAtlasiQ93079.
PRIDEiQ93079.
TopDownProteomicsiQ93079.

PTM databases

iPTMnetiQ93079.
PhosphoSiteiQ93079.
SwissPalmiQ93079.

Expressioni

Gene expression databases

BgeeiENSG00000197459.
CleanExiHS_HIST1H2BH.
GenevisibleiQ93079. HS.

Organism-specific databases

HPAiHPA042205.
HPA043013.
HPA048671.

Interactioni

Subunit structurei

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.

Protein-protein interaction databases

BioGridi113941. 10 interactions.
IntActiQ93079. 8 interactions.
MINTiMINT-4829860.
STRINGi9606.ENSP00000348706.

Structurei

3D structure databases

ProteinModelPortaliQ93079.
SMRiQ93079. Positions 5-126.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H2B family.Curated

Phylogenomic databases

eggNOGiKOG1744. Eukaryota.
ENOG4111NV5. LUCA.
GeneTreeiENSGT00760000118976.
HOGENOMiHOG000231213.
HOVERGENiHBG007774.
InParanoidiQ93079.
KOiK11252.
OMAiNSERWAV.
OrthoDBiEOG091G0XGD.
PhylomeDBiQ93079.
TreeFamiTF300212.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_H2A/H2B/H3.
IPR000558. Histone_H2B.
[Graphical view]
PANTHERiPTHR23428. PTHR23428. 1 hit.
PfamiPF00125. Histone. 1 hit.
[Graphical view]
PRINTSiPR00621. HISTONEH2B.
SMARTiSM00427. H2B. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00357. HISTONE_H2B. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q93079-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPDPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH
60 70 80 90 100
PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRSTI TSREIQTAVR
110 120
LLLPGELAKH AVSEGTKAVT KYTSSK
Length:126
Mass (Da):13,892
Last modified:January 23, 2007 - v3
Checksum:iFAE0F79FF4BF703D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z80781 Genomic DNA. Translation: CAB02543.1.
AF531291 Genomic DNA. Translation: AAN06691.1.
AK312052 mRNA. Translation: BAG34988.1.
AL031777 Genomic DNA. Translation: CAB39185.1.
CH471087 Genomic DNA. Translation: EAW55552.1.
BC096116 mRNA. Translation: AAH96116.1.
BC096117 mRNA. Translation: AAH96117.1.
BC096118 mRNA. Translation: AAH96118.1.
BC096119 mRNA. Translation: AAH96119.1.
CCDSiCCDS4601.1.
RefSeqiNP_003515.1. NM_003524.2.
UniGeneiHs.247815.

Genome annotation databases

EnsembliENST00000619466; ENSP00000479169; ENSG00000275713.
GeneIDi8345.
KEGGihsa:8345.
UCSCiuc003nhh.4. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z80781 Genomic DNA. Translation: CAB02543.1.
AF531291 Genomic DNA. Translation: AAN06691.1.
AK312052 mRNA. Translation: BAG34988.1.
AL031777 Genomic DNA. Translation: CAB39185.1.
CH471087 Genomic DNA. Translation: EAW55552.1.
BC096116 mRNA. Translation: AAH96116.1.
BC096117 mRNA. Translation: AAH96117.1.
BC096118 mRNA. Translation: AAH96118.1.
BC096119 mRNA. Translation: AAH96119.1.
CCDSiCCDS4601.1.
RefSeqiNP_003515.1. NM_003524.2.
UniGeneiHs.247815.

3D structure databases

ProteinModelPortaliQ93079.
SMRiQ93079. Positions 5-126.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi113941. 10 interactions.
IntActiQ93079. 8 interactions.
MINTiMINT-4829860.
STRINGi9606.ENSP00000348706.

PTM databases

iPTMnetiQ93079.
PhosphoSiteiQ93079.
SwissPalmiQ93079.

Polymorphism and mutation databases

BioMutaiHIST1H2BH.
DMDMi7387739.

Proteomic databases

EPDiQ93079.
MaxQBiQ93079.
PaxDbiQ93079.
PeptideAtlasiQ93079.
PRIDEiQ93079.
TopDownProteomicsiQ93079.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000619466; ENSP00000479169; ENSG00000275713.
GeneIDi8345.
KEGGihsa:8345.
UCSCiuc003nhh.4. human.

Organism-specific databases

CTDi8345.
GeneCardsiHIST1H2BH.
HGNCiHGNC:4755. HIST1H2BH.
HPAiHPA042205.
HPA043013.
HPA048671.
MIMi602806. gene.
neXtProtiNX_Q93079.
PharmGKBiPA29130.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1744. Eukaryota.
ENOG4111NV5. LUCA.
GeneTreeiENSGT00760000118976.
HOGENOMiHOG000231213.
HOVERGENiHBG007774.
InParanoidiQ93079.
KOiK11252.
OMAiNSERWAV.
OrthoDBiEOG091G0XGD.
PhylomeDBiQ93079.
TreeFamiTF300212.

Enzyme and pathway databases

ReactomeiR-HSA-1221632. Meiotic synapsis.
R-HSA-171306. Packaging Of Telomere Ends.
R-HSA-201722. Formation of the beta-catenin:TCF transactivating complex.
R-HSA-212300. PRC2 methylates histones and DNA.
R-HSA-2299718. Condensation of Prophase Chromosomes.
R-HSA-2559580. Oxidative Stress Induced Senescence.
R-HSA-2559582. Senescence-Associated Secretory Phenotype (SASP).
R-HSA-2559586. DNA Damage/Telomere Stress Induced Senescence.
R-HSA-3214815. HDACs deacetylate histones.
R-HSA-3214847. HATs acetylate histones.
R-HSA-427359. SIRT1 negatively regulates rRNA Expression.
R-HSA-427389. ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression.
R-HSA-427413. NoRC negatively regulates rRNA expression.
R-HSA-5250924. B-WICH complex positively regulates rRNA expression.
R-HSA-5334118. DNA methylation.
R-HSA-5578749. Transcriptional regulation by small RNAs.
R-HSA-5617472. Activation of anterior HOX genes in hindbrain development during early embryogenesis.
R-HSA-5625886. Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3.
R-HSA-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
R-HSA-5693571. Nonhomologous End-Joining (NHEJ).
R-HSA-5693607. Processing of DNA double-strand break ends.
R-HSA-606279. Deposition of new CENPA-containing nucleosomes at the centromere.
R-HSA-69473. G2/M DNA damage checkpoint.
R-HSA-73728. RNA Polymerase I Promoter Opening.
R-HSA-73777. RNA Polymerase I Chain Elongation.
R-HSA-912446. Meiotic recombination.
R-HSA-977225. Amyloid fiber formation.

Miscellaneous databases

ChiTaRSiHIST1H2BH. human.
GeneWikiiHIST1H2BH.
GenomeRNAii8345.
PROiQ93079.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000197459.
CleanExiHS_HIST1H2BH.
GenevisibleiQ93079. HS.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_H2A/H2B/H3.
IPR000558. Histone_H2B.
[Graphical view]
PANTHERiPTHR23428. PTHR23428. 1 hit.
PfamiPF00125. Histone. 1 hit.
[Graphical view]
PRINTSiPR00621. HISTONEH2B.
SMARTiSM00427. H2B. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00357. HISTONE_H2B. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiH2B1H_HUMAN
AccessioniPrimary (citable) accession number: Q93079
Secondary accession number(s): B2R541, Q4VB74
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: January 23, 2007
Last modified: September 7, 2016
This is version 156 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 6
    Human chromosome 6: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.