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Protein

Histone H2B type 1-J

Gene

HIST1H2BJ

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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.
Has broad antibacterial activity. May contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.

GO - Molecular functioni

  • DNA binding Source: GO_Central
  • lipopolysaccharide binding Source: UniProtKB
  • protein heterodimerization activity Source: InterPro

GO - Biological processi

  • antibacterial humoral response Source: UniProtKB
  • antimicrobial humoral immune response mediated by antimicrobial peptide Source: UniProtKB
  • defense response to Gram-negative bacterium Source: UniProtKB
  • defense response to Gram-positive bacterium Source: UniProtKB
  • innate immune response in mucosa Source: UniProtKB
  • killing of cells of other organism Source: UniProtKB
  • negative regulation of tumor necrosis factor-mediated signaling pathway Source: UniProtKB
  • nucleosome assembly Source: GO_Central
  • protein ubiquitination Source: Reactome

Keywordsi

Molecular functionAntibiotic, Antimicrobial, 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-5689880 Ub-specific processing proteases
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-8866654 E3 ubiquitin ligases ubiquitinate target proteins
R-HSA-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-HSA-8939236 RUNX1 regulates transcription of genes involved in differentiation of HSCs
R-HSA-9018519 Estrogen-dependent gene expression
R-HSA-912446 Meiotic recombination
R-HSA-977225 Amyloid fiber formation

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H2B type 1-J
Alternative name(s):
Histone H2B.1
Histone H2B.r
Short name:
H2B/r
Gene namesi
Name:HIST1H2BJ
Synonyms:H2BFR
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

EuPathDBiHostDB:ENSG00000124635.8
HGNCiHGNC:4761 HIST1H2BJ
MIMi615044 gene
neXtProtiNX_P06899

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi8970
OpenTargetsiENSG00000124635
PharmGKBiPA29136

Polymorphism and mutation databases

BioMutaiHIST1H2BJ
DMDMi7404367

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity5 Publications
ChainiPRO_00000718362 – 126Histone H2B type 1-JAdd BLAST125

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylprolineBy similarity1
Modified residuei6N6-(2-hydroxyisobutyryl)lysine; alternate1 Publication1
Modified residuei6N6-(beta-hydroxybutyryl)lysine; alternate1 Publication1
Modified residuei6N6-acetyllysine; alternate2 Publications1
Modified residuei6N6-butyryllysine; alternate1 Publication1
Modified residuei6N6-crotonyllysine; alternate1 Publication1
Cross-linki6Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateBy similarity
Modified residuei12N6-(beta-hydroxybutyryl)lysine; alternate1 Publication1
Modified residuei12N6-acetyllysine; alternate1 Publication1
Modified residuei12N6-crotonyllysine; alternate1 Publication1
Modified residuei13N6-(2-hydroxyisobutyryl)lysine; alternate1 Publication1
Modified residuei13N6-acetyllysine; alternate2 Publications1
Modified residuei13N6-crotonyllysine; alternate1 Publication1
Modified residuei15Phosphoserine; by STK4/MST11 Publication1
Modified residuei16N6-acetyllysine; alternate2 Publications1
Modified residuei16N6-crotonyllysine; alternate1 Publication1
Modified residuei17N6-(beta-hydroxybutyryl)lysine; alternate1 Publication1
Modified residuei17N6-acetyllysine; alternate1 Publication1
Modified residuei17N6-crotonyllysine; alternate1 Publication1
Modified residuei21N6-(2-hydroxyisobutyryl)lysine; alternate1 Publication1
Modified residuei21N6-(beta-hydroxybutyryl)lysine; alternate1 Publication1
Modified residuei21N6-acetyllysine; alternate2 Publications1
Modified residuei21N6-butyryllysine; alternate1 Publication1
Modified residuei21N6-crotonyllysine; alternate1 Publication1
Cross-linki21Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateBy similarity
Modified residuei24N6-(2-hydroxyisobutyryl)lysine; alternate1 Publication1
Modified residuei24N6-acetyllysine; alternateBy similarity1
Modified residuei24N6-crotonyllysine; alternate1 Publication1
Modified residuei25N6-(2-hydroxyisobutyryl)lysine1 Publication1
Modified residuei35N6-(2-hydroxyisobutyryl)lysine; alternate1 Publication1
Modified residuei35N6-(beta-hydroxybutyryl)lysine; alternate1 Publication1
Modified residuei35N6-crotonyllysine; alternate1 Publication1
Modified residuei35N6-succinyllysine; alternate1 Publication1
Cross-linki35Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate1 Publication
Modified residuei37Phosphoserine; by AMPKBy similarity1
Modified residuei44N6-(2-hydroxyisobutyryl)lysine1 Publication1
Modified residuei47N6-(2-hydroxyisobutyryl)lysine; alternate1 Publication1
Modified residuei47N6-methyllysine; alternate1 Publication1
Modified residuei58N6,N6-dimethyllysine; alternate1 Publication1
Modified residuei58N6-(2-hydroxyisobutyryl)lysine; alternate1 Publication1
Modified residuei80Dimethylated arginineBy similarity1
Modified residuei86N6,N6,N6-trimethyllysine; alternateBy similarity1
Modified residuei86N6-(2-hydroxyisobutyryl)lysine; alternate1 Publication1
Modified residuei86N6-(beta-hydroxybutyryl)lysine; alternate1 Publication1
Modified residuei86N6-acetyllysine; alternateBy similarity1
Modified residuei87Omega-N-methylarginineBy similarity1
Modified residuei93Omega-N-methylarginineBy similarity1
Modified residuei109N6-(2-hydroxyisobutyryl)lysine; alternate1 Publication1
Modified residuei109N6-methyllysine; alternate1 Publication1
Glycosylationi113O-linked (GlcNAc) serineBy similarity1
Modified residuei116PhosphothreonineBy similarity1
Modified residuei117N6-(2-hydroxyisobutyryl)lysine; alternate1 Publication1
Modified residuei117N6-(beta-hydroxybutyryl)lysine; alternate1 Publication1
Modified residuei117N6-malonyllysine; alternate1 Publication1
Modified residuei117N6-methylated lysine; alternateBy similarity1
Modified residuei117N6-succinyllysine; alternate1 Publication1
Modified residuei121N6-(2-hydroxyisobutyryl)lysine; alternate1 Publication1
Modified residuei121N6-(beta-hydroxybutyryl)lysine; alternate1 Publication1
Modified residuei121N6-succinyllysine; alternate1 Publication1
Cross-linki121Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate3 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.2 Publications
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, Hydroxylation, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiP06899
MaxQBiP06899
PaxDbiP06899
PeptideAtlasiP06899
PRIDEiP06899
TopDownProteomicsiP06899

PTM databases

iPTMnetiP06899
PhosphoSitePlusiP06899
SwissPalmiP06899

Expressioni

Gene expression databases

BgeeiENSG00000124635
CleanExiHS_HIST1H2BJ
ExpressionAtlasiP06899 baseline and differential

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. Heterodimer HIST1H2BJ and H2AFZ interacts with VPS72 (via N-terminal domain) (PubMed:26974126).2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
HIST1H2ABP049089EBI-6150252,EBI-358971

GO - Molecular functioni

Protein-protein interaction databases

BioGridi114460, 30 interactors
DIPiDIP-421N
IntActiP06899, 10 interactors
MINTiP06899
STRINGi9606.ENSP00000342886

Structurei

Secondary structure

1126
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi39 – 49Combined sources11
Beta strandi54 – 56Combined sources3
Helixi57 – 83Combined sources27
Turni84 – 86Combined sources3
Beta strandi88 – 90Combined sources3
Helixi92 – 102Combined sources11
Helixi105 – 124Combined sources20

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2RVQNMR-D1-126[»]
3A6NX-ray2.70D/H1-126[»]
3AFAX-ray2.50D/H1-126[»]
3AN2X-ray3.60D/H1-126[»]
3AV1X-ray2.50D/H1-126[»]
3AV2X-ray2.80D/H1-126[»]
3AYWX-ray2.90D/H1-126[»]
3AZEX-ray3.00D/H1-126[»]
3AZFX-ray2.70D/H1-126[»]
3AZGX-ray2.40D/H1-126[»]
3AZHX-ray3.49D/H1-126[»]
3AZIX-ray2.70D/H1-126[»]
3AZJX-ray2.89D/H1-126[»]
3AZKX-ray3.20D/H1-126[»]
3AZLX-ray2.70D/H1-126[»]
3AZMX-ray2.89D/H1-126[»]
3AZNX-ray3.00D/H1-126[»]
3W96X-ray3.00D/H1-126[»]
3W97X-ray3.20D/H26-126[»]
3W98X-ray3.42D/H1-126[»]
3W99X-ray3.00D/H1-126[»]
3WA9X-ray3.07D/H1-126[»]
3WAAX-ray3.20D/H1-126[»]
3WTPX-ray2.67D/H1-126[»]
4CAYX-ray1.48B31-126[»]
4YM5X-ray4.00D/H1-126[»]
4YM6X-ray3.51D/H1-126[»]
4Z5TX-ray2.80D/H1-126[»]
5AV5X-ray2.40D/H1-126[»]
5AV6X-ray2.20D/H1-126[»]
5AV8X-ray2.20D/H1-126[»]
5AV9X-ray2.20D/H1-126[»]
5AVBX-ray2.40D/H1-126[»]
5AVCX-ray2.40D/H1-126[»]
5AY8X-ray2.80D/H1-126[»]
5B0YX-ray2.56D/H1-126[»]
5B0ZX-ray1.99D/H1-126[»]
5B24X-ray3.60D/H1-126[»]
5B2IX-ray3.00D/H1-126[»]
5B2JX-ray2.60D/H1-126[»]
5B31X-ray2.20D/H1-126[»]
5B32X-ray2.35D/H1-126[»]
5B33X-ray2.92D/H1-126[»]
5B40X-ray3.33D/H1-126[»]
5CPIX-ray2.90D/H1-126[»]
5CPJX-ray3.15D/H1-126[»]
5CPKX-ray2.63D/H1-126[»]
5FUGX-ray2.70B/E/H/K31-126[»]
5GSEX-ray3.14D/H/N1-126[»]
5GTCX-ray2.70D/H1-126[»]
5GXQX-ray2.85D/H1-126[»]
5JRGX-ray2.50D/H1-126[»]
5VEYNMR-A34-124[»]
5X7XX-ray2.18D/H1-126[»]
5XF3X-ray2.60D/H1-126[»]
5XF4X-ray2.87D/H1-126[»]
5XF5X-ray2.82D/H1-126[»]
6BUZelectron microscopy3.92D/H1-126[»]
ProteinModelPortaliP06899
SMRiP06899
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP06899

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H2B family.Curated

Phylogenomic databases

eggNOGiKOG1744 Eukaryota
ENOG4111NV5 LUCA
GeneTreeiENSGT00760000118976
HOGENOMiHOG000231213
HOVERGENiHBG007774
InParanoidiP06899
KOiK11252
OMAiANSEGMK
OrthoDBiEOG091G0XGD
PhylomeDBiP06899
TreeFamiTF300212

Family and domain databases

Gene3Di1.10.20.10, 1 hit
InterProiView protein in InterPro
IPR009072 Histone-fold
IPR007125 Histone_H2A/H2B/H3
IPR000558 Histone_H2B
PANTHERiPTHR23428 PTHR23428, 1 hit
PfamiView protein in Pfam
PF00125 Histone, 1 hit
PRINTSiPR00621 HISTONEH2B
SMARTiView protein in SMART
SM00427 H2B, 1 hit
SUPFAMiSSF47113 SSF47113, 1 hit
PROSITEiView protein in PROSITE
PS00357 HISTONE_H2B, 1 hit

Sequencei

Sequence statusi: Complete.

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

P06899-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH
60 70 80 90 100
PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRSTI TSREIQTAVR
110 120
LLLPGELAKH AVSEGTKAVT KYTSAK
Length:126
Mass (Da):13,904
Last modified:January 23, 2007 - v3
Checksum:i0408C881ABBE6647
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti29 – 33KRKRS → SAAH in CAA24950 (PubMed:6647026).Curated5

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X00088 Genomic DNA Translation: CAA24950.1
AF531293 Genomic DNA Translation: AAN06693.1
AK311849 mRNA Translation: BAG34791.1
AL021807 Genomic DNA No translation available.
CH471081 Genomic DNA Translation: EAX03080.1
CCDSiCCDS4618.1
PIRiA26318 HSHUB1
S65409
RefSeqiNP_066402.2, NM_021058.3
UniGeneiHs.591807
Hs.656567

Genome annotation databases

EnsembliENST00000339812; ENSP00000342886; ENSG00000124635
ENST00000607124; ENSP00000476136; ENSG00000124635
GeneIDi8970
KEGGihsa:8970
UCSCiuc003niv.4 human

Similar proteinsi

Entry informationi

Entry nameiH2B1J_HUMAN
AccessioniPrimary (citable) accession number: P06899
Secondary accession number(s): B2R4J4, O60816
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: January 23, 2007
Last modified: May 23, 2018
This is version 180 of the entry and version 3 of the sequence. See 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

3D-structure, 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

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