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Protein

Histone H2B 1/2/3/4/6

Gene

H2B-I

more
Organism
Gallus gallus (Chicken)
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.1 Publication
Has broad-spectrum antibacterial activity. May be important in the antimicrobial defenses of chick reproductive system during follicle development in the ovary and egg formation in the oviduct.1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Antibiotic, Antimicrobial

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiREACT_275071. HATs acetylate histones.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H2B 1/2/3/4/6
Alternative name(s):
H2B I
H2B II
H2B III
H2B IV
H2B VI
Gene namesi
Name:H2B-I
AND
Name:H2B-II
AND
Name:H2B-III
AND
Name:H2B-IV
AND
Name:H2B-VI
OrganismiGallus gallus (Chicken)
Taxonomic identifieri9031 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiArchelosauriaArchosauriaDinosauriaSaurischiaTheropodaCoelurosauriaAvesNeognathaeGalloanseraeGalliformesPhasianidaePhasianinaeGallus
ProteomesiUP000000539 Componenti: Chromosome 1

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 methioninei1 – 11Removed2 Publications
Chaini2 – 126125Histone H2B 1/2/3/4/6PRO_0000071846Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei6 – 61N6-acetyllysine1 Publication
Modified residuei13 – 131N6-acetyllysine1 Publication
Modified residuei15 – 151Phosphoserine1 Publication
Modified residuei16 – 161N6-acetyllysine1 Publication
Modified residuei21 – 211N6-acetyllysine1 Publication
Cross-linki121 – 121Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication

Post-translational modificationi

Monoubiquitination of Lys-121 by the BRE1 gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation.By similarity
Phosphorylated on Ser-15 during apoptosis; which facilitates apoptotic chromatin condensation.1 Publication

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiP0C1H3.

Expressioni

Gene expression databases

ExpressionAtlasiP0C1H3. baseline.

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

BioGridi679231. 3 interactions.
IntActiP0C1H3. 1 interaction.
STRINGi9031.ENSGALP00000037300.

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 – 12420Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2AROX-ray2.10B/F1-126[»]
ProteinModelPortaliP0C1H3.
SMRiP0C1H3. Positions 19-126.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0C1H3.

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H2B family.Curated

Phylogenomic databases

eggNOGiNOG303883.
GeneTreeiENSGT00760000118976.
HOGENOMiHOG000231213.
HOVERGENiHBG007774.
InParanoidiP0C1H3.
KOiK11252.
OMAiAKTHKEA.
PhylomeDBiP0C1H3.
TreeFamiTF300212.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_core_D.
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.

P0C1H3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPEPAKSAPA PKKGSKKAVT KTQKKGDKKR KKSRKESYSI YVYKVLKQVH
60 70 80 90 100
PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRSTI TSREIQTAVR
110 120
LLLPGELAKH AVSEGTKAVT KYTSSK
Length:126
Mass (Da):13,922
Last modified:January 23, 2007 - v2
Checksum:i908F039A02A3400D
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti14 – 141G → A in CAA28745 (PubMed:3822819).Curated
Sequence conflicti36 – 361E → A in CAA28747 (PubMed:3822819).Curated
Sequence conflicti62 – 621I → S AA sequence (PubMed:7074112).Curated
Sequence conflicti123 – 1231T → I in CAA28751 (PubMed:3822819).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
V00415 Genomic DNA. Translation: CAA23706.1.
X05094 Genomic DNA. Translation: CAA28745.1.
X05095 Genomic DNA. Translation: CAA28746.1.
X05096 Genomic DNA. Translation: CAA28747.1.
X05097 Genomic DNA. Translation: CAA28748.1.
X05098 Genomic DNA. Translation: CAA28749.1.
X05100 Genomic DNA. Translation: CAA28751.1.
X57263 Genomic DNA. Translation: CAA40537.1.
X07763 Genomic DNA. Translation: CAA30590.1.
X07766 Genomic DNA. Translation: CAA30596.1.
PIRiB26399.
S14510. HSCH22.
RefSeqiNP_001073188.1. NM_001079720.1.
XP_001232985.1. XM_001232984.2.
XP_001233227.1. XM_001233226.3.
XP_001233337.1. XM_001233336.3.
UniGeneiGga.39843.

Genome annotation databases

EnsembliENSGALT00000021778; ENSGALP00000021742; ENSGALG00000027174.
ENSGALT00000042841; ENSGALP00000042437; ENSGALG00000027594.
ENSGALT00000043224; ENSGALP00000042501; ENSGALG00000027571.
GeneIDi417956.
769973.
770188.
770267.
KEGGigga:417956.
gga:769973.
gga:770188.
gga:770267.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
V00415 Genomic DNA. Translation: CAA23706.1.
X05094 Genomic DNA. Translation: CAA28745.1.
X05095 Genomic DNA. Translation: CAA28746.1.
X05096 Genomic DNA. Translation: CAA28747.1.
X05097 Genomic DNA. Translation: CAA28748.1.
X05098 Genomic DNA. Translation: CAA28749.1.
X05100 Genomic DNA. Translation: CAA28751.1.
X57263 Genomic DNA. Translation: CAA40537.1.
X07763 Genomic DNA. Translation: CAA30590.1.
X07766 Genomic DNA. Translation: CAA30596.1.
PIRiB26399.
S14510. HSCH22.
RefSeqiNP_001073188.1. NM_001079720.1.
XP_001232985.1. XM_001232984.2.
XP_001233227.1. XM_001233226.3.
XP_001233337.1. XM_001233336.3.
UniGeneiGga.39843.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2AROX-ray2.10B/F1-126[»]
ProteinModelPortaliP0C1H3.
SMRiP0C1H3. Positions 19-126.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi679231. 3 interactions.
IntActiP0C1H3. 1 interaction.
STRINGi9031.ENSGALP00000037300.

Proteomic databases

PaxDbiP0C1H3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSGALT00000021778; ENSGALP00000021742; ENSGALG00000027174.
ENSGALT00000042841; ENSGALP00000042437; ENSGALG00000027594.
ENSGALT00000043224; ENSGALP00000042501; ENSGALG00000027571.
GeneIDi417956.
769973.
770188.
770267.
KEGGigga:417956.
gga:769973.
gga:770188.
gga:770267.

Organism-specific databases

CTDi417956.
769973.
770188.
770267.

Phylogenomic databases

eggNOGiNOG303883.
GeneTreeiENSGT00760000118976.
HOGENOMiHOG000231213.
HOVERGENiHBG007774.
InParanoidiP0C1H3.
KOiK11252.
OMAiAKTHKEA.
PhylomeDBiP0C1H3.
TreeFamiTF300212.

Enzyme and pathway databases

ReactomeiREACT_275071. HATs acetylate histones.

Miscellaneous databases

EvolutionaryTraceiP0C1H3.
NextBioi20821182.
PROiP0C1H3.

Gene expression databases

ExpressionAtlasiP0C1H3. baseline.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_core_D.
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...

Publicationsi

  1. "Complete nucleotide sequence of a chicken H2B histone gene."
    Grandy D.K., Engel J.D., Dodgson J.B.
    J. Biol. Chem. 257:8577-8580(1982) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Structure and organization of the chicken H2B histone gene family."
    Grandy D.K., Dodgson J.B.
    Nucleic Acids Res. 15:1063-1080(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: White leghorn.
    Tissue: Blood.
  3. "Nucleotide sequence of a member of the chicken H2B histone-encoding gene family."
    Nakayama T., Setoguchi Y.
    Gene 98:299-300(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  4. "Organization of the chicken histone genes in a major gene cluster and generation of an almost complete set of the core histone protein sequences."
    Takami Y., Higashio M., Fukuoka T., Takechi S., Nakayama T.
    DNA Res. 3:95-99(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], NOMENCLATURE.
    Strain: White leghorn.
  5. "Conservation of histone H2A/H2B intergene regions: a role for the H2B specific element in divergent transcription."
    Sturm R.A., Dalton S., Wells J.R.E.
    Nucleic Acids Res. 16:8571-8586(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  6. "The complete amino-acid sequence of histone H2B from erythrocytes of the adult domestic fowl Gallus domesticus."
    van Helden P., Strickland W.N., Strickland M., von Holt C.
    Biochim. Biophys. Acta 703:17-20(1982) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-126.
  7. "Histone H2B variants from the erythrocytes of an amphibian, a reptile and a bird."
    van Helden P., Strickland W.N., Brandt W.F., von Holt C.
    Biochim. Biophys. Acta 533:278-281(1978) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-30 AND 62-90.
    Tissue: Erythrocyte.
  8. "Ubiquitinated histone H2B is preferentially located in transcriptionally active chromatin."
    Nickel B.E., Allis C.D., Davie J.R.
    Biochemistry 28:958-963(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION.
  9. "Apoptotic phosphorylation of histone H2B is mediated by mammalian sterile twenty kinase."
    Cheung W.L., Ajiro K., Samejima K., Kloc M., Cheung P., Mizzen C.A., Beeser A., Etkin L.D., Chernoff J., Earnshaw W.C., Allis C.D.
    Cell 113:507-517(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT SER-15.
  10. "Acetylation of histone H2B mirrors that of H4 and H3 at the chicken beta-globin locus but not at housekeeping genes."
    Myers F.A., Chong W., Evans D.R., Thorne A.W., Crane-Robinson C.
    J. Biol. Chem. 278:36315-36322(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION AT LYS-6; LYS-13; LYS-16 AND LYS-21.
  11. Cited for: FUNCTION AS AN ANTIBIOTIC, IDENTIFICATION BY MASS SPECTROMETRY.
  12. "The nucleosomal core histone octamer at 3.1 A resolution: a tripartite protein assembly and a left-handed superhelix."
    Arents G., Burlingame R.W., Wang B.-C., Love W.E., Moudrianakis E.N.
    Proc. Natl. Acad. Sci. U.S.A. 88:10148-10152(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS).

Entry informationi

Entry nameiH2B1_CHICK
AccessioniPrimary (citable) accession number: P0C1H3
Secondary accession number(s): P02279, Q92067
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 11, 2006
Last sequence update: January 23, 2007
Last modified: June 24, 2015
This is version 77 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.