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Protein

Histone H2B type 3-A

Gene

Hist3h2ba

Organism
Mus musculus (Mouse)
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

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiR-MMU-1221632. Meiotic synapsis.
R-MMU-1221633. Meiotic Synapsis.
R-MMU-3214847. HATs acetylate histones.
R-MMU-427389. ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression.
R-MMU-427413. NoRC negatively regulates rRNA expression.
R-MMU-5334118. DNA methylation.
R-MMU-5617472. Activation of anterior HOX genes in hindbrain development during early embryogenesis.
R-MMU-573389. NoRC negatively regulates rRNA expression.
R-MMU-912497. Meiotic Recombination.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H2B type 3-A
Gene namesi
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 11

Organism-specific databases

MGIiMGI:1925553. Hist3h2ba.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 126125Histone H2B type 3-APRO_0000244837Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylprolineBy similarity
Modified residuei12 – 121N6-acetyllysine; alternateBy similarity
Modified residuei12 – 121N6-crotonyllysine; alternate1 Publication
Modified residuei13 – 131N6-acetyllysine; alternateBy similarity
Modified residuei13 – 131N6-crotonyllysine; alternate1 Publication
Modified residuei15 – 151Phosphoserine; by STK4/MST12 Publications
Modified residuei16 – 161N6-acetyllysine; alternateBy similarity
Modified residuei16 – 161N6-crotonyllysine; alternate1 Publication
Modified residuei17 – 171N6-acetyllysine; alternateBy similarity
Modified residuei17 – 171N6-crotonyllysine; alternate1 Publication
Modified residuei21 – 211N6-acetyllysine; alternateBy similarity
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); alternateBy similarity
Modified residuei37 – 371Phosphoserine; by AMPK1 Publication
Modified residuei47 – 471N6-methyllysineBy similarity
Modified residuei58 – 581N6,N6-dimethyllysineBy similarity
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-methyllysineBy similarity
Modified residuei116 – 1161PhosphothreonineBy similarity
Modified residuei117 – 1171N6-methylated lysineBy similarity
Cross-linki121 – 121Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity

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 (By similarity).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. Phosphorylation at Ser-37 (H2BS36ph) by AMPK in response to stress promotes transcription.3 Publications
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, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ9D2U9.
MaxQBiQ9D2U9.
PaxDbiQ9D2U9.
PeptideAtlasiQ9D2U9.
PRIDEiQ9D2U9.

PTM databases

iPTMnetiQ9D2U9.
PhosphoSiteiQ9D2U9.

Expressioni

Gene expression databases

BgeeiENSMUSG00000056895.
CleanExiMM_HIST3H2BA.
GenevisibleiQ9D2U9. MM.

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.1 Publication

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000076397.

Structurei

Secondary structure

1
126
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi39 – 4911Combined sources
Helixi57 – 8428Combined sources
Beta strandi88 – 903Combined sources
Helixi92 – 10211Combined sources
Helixi105 – 12218Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1U35X-ray3.00D/H1-126[»]
2F8NX-ray2.90D1-126[»]
ProteinModelPortaliQ9D2U9.
SMRiQ9D2U9. Positions 5-126.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9D2U9.

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H2B family.Curated

Phylogenomic databases

eggNOGiKOG1744. Eukaryota.
ENOG4111NV5. LUCA.
GeneTreeiENSGT00760000118976.
HOGENOMiHOG000231213.
HOVERGENiHBG007774.
InParanoidiQ9D2U9.
KOiK11252.
OMAiHCCSSEP.
OrthoDBiEOG091G0XGD.
PhylomeDBiQ9D2U9.
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.

Q9D2U9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPEPSRSTPA PKKGSKKAIT KAQKKDGKKR KRGRKESYSI YVYKVLKQVH
60 70 80 90 100
PDTGISSKAM GIMNSFVNDI FERIASEASR LAHYNKRSTI TSREVQTAVR
110 120
LLLPGELAKH AVSEGTKAVT KYTSSK
Length:126
Mass (Da):13,994
Last modified:January 23, 2007 - v3
Checksum:iDC1CF72D9457CC56
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY158942 Genomic DNA. Translation: AAO06252.1.
AK018765 mRNA. Translation: BAB31395.1.
BC051921 mRNA. Translation: AAH51921.1.
CCDSiCCDS24754.1.
RefSeqiNP_084358.1. NM_030082.4.
UniGeneiMm.28022.

Genome annotation databases

EnsembliENSMUST00000078267; ENSMUSP00000076397; ENSMUSG00000056895.
GeneIDi78303.
KEGGimmu:78303.
UCSCiuc007jcr.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY158942 Genomic DNA. Translation: AAO06252.1.
AK018765 mRNA. Translation: BAB31395.1.
BC051921 mRNA. Translation: AAH51921.1.
CCDSiCCDS24754.1.
RefSeqiNP_084358.1. NM_030082.4.
UniGeneiMm.28022.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1U35X-ray3.00D/H1-126[»]
2F8NX-ray2.90D1-126[»]
ProteinModelPortaliQ9D2U9.
SMRiQ9D2U9. Positions 5-126.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000076397.

PTM databases

iPTMnetiQ9D2U9.
PhosphoSiteiQ9D2U9.

Proteomic databases

EPDiQ9D2U9.
MaxQBiQ9D2U9.
PaxDbiQ9D2U9.
PeptideAtlasiQ9D2U9.
PRIDEiQ9D2U9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000078267; ENSMUSP00000076397; ENSMUSG00000056895.
GeneIDi78303.
KEGGimmu:78303.
UCSCiuc007jcr.2. mouse.

Organism-specific databases

CTDi337872.
MGIiMGI:1925553. Hist3h2ba.

Phylogenomic databases

eggNOGiKOG1744. Eukaryota.
ENOG4111NV5. LUCA.
GeneTreeiENSGT00760000118976.
HOGENOMiHOG000231213.
HOVERGENiHBG007774.
InParanoidiQ9D2U9.
KOiK11252.
OMAiHCCSSEP.
OrthoDBiEOG091G0XGD.
PhylomeDBiQ9D2U9.
TreeFamiTF300212.

Enzyme and pathway databases

ReactomeiR-MMU-1221632. Meiotic synapsis.
R-MMU-1221633. Meiotic Synapsis.
R-MMU-3214847. HATs acetylate histones.
R-MMU-427389. ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression.
R-MMU-427413. NoRC negatively regulates rRNA expression.
R-MMU-5334118. DNA methylation.
R-MMU-5617472. Activation of anterior HOX genes in hindbrain development during early embryogenesis.
R-MMU-573389. NoRC negatively regulates rRNA expression.
R-MMU-912497. Meiotic Recombination.

Miscellaneous databases

EvolutionaryTraceiQ9D2U9.
PROiQ9D2U9.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000056895.
CleanExiMM_HIST3H2BA.
GenevisibleiQ9D2U9. MM.

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 nameiH2B3A_MOUSE
AccessioniPrimary (citable) accession number: Q9D2U9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 11, 2006
Last sequence update: January 23, 2007
Last modified: September 7, 2016
This is version 129 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Miscellaneous

The human orthologous protein seems not to exist.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.