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Protein

Histone H4

Gene

H4-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.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi17 – 215

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiREACT_275071. HATs acetylate histones.
REACT_276260. DNA methylation.
REACT_277792. RNA Polymerase I Chain Elongation.
REACT_286644. Meiotic recombination.
REACT_299305. PRC2 methylates histones and DNA.
REACT_299693. PKMTs methylate histone lysines.
REACT_310543. RMTs methylate histone arginines.
REACT_316866. Transcriptional regulation by small RNAs.
REACT_316940. SIRT1 negatively regulates rRNA Expression.
REACT_322027. RNA Polymerase I Promoter Opening.
REACT_334370. Condensation of Prophase Chromosomes.
REACT_339698. Deposition of new CENPA-containing nucleosomes at the centromere.
REACT_340836. NoRC negatively regulates rRNA expression.
REACT_342239. Senescence-Associated Secretory Phenotype (SASP).
REACT_348443. Oxidative Stress Induced Senescence.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H4
Gene namesi
Name:H4-I
AND
Name:H4-II
AND
Name:H4-III
AND
Name:H4-IV
AND
Name:H4-V
AND
Name:H4-VI
AND
Name:H4-VII
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 – 11RemovedBy similarity
Chaini2 – 103102Histone H4PRO_0000158296Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineBy similarity
Modified residuei2 – 21PhosphoserineBy similarity
Modified residuei4 – 41Asymmetric dimethylarginine; by PRMT1; alternateBy similarity
Modified residuei4 – 41Citrulline; alternateBy similarity
Modified residuei4 – 41Omega-N-methylarginine; by PRMT1; alternateBy similarity
Modified residuei4 – 41Symmetric dimethylarginine; by PRMT5 and PRMT7; alternateBy similarity
Modified residuei6 – 61N6-acetyllysineBy similarity
Modified residuei9 – 91N6-acetyllysineBy similarity
Modified residuei13 – 131N6-acetyllysineBy similarity
Modified residuei17 – 171N6-acetyllysineBy similarity
Modified residuei21 – 211N6,N6,N6-trimethyllysine; alternateBy similarity
Modified residuei21 – 211N6,N6-dimethyllysine; alternateBy similarity
Modified residuei21 – 211N6-methylated lysineBy similarity
Modified residuei21 – 211N6-methyllysine; alternateBy similarity
Modified residuei32 – 321N6-acetyllysineBy similarity
Modified residuei48 – 481Phosphoserine; by PAK2By similarity
Modified residuei52 – 521PhosphotyrosineBy similarity
Modified residuei60 – 601N6-acetyllysineBy similarity
Modified residuei80 – 801N6-acetyllysineBy similarity
Modified residuei89 – 891PhosphotyrosineBy similarity
Modified residuei92 – 921N6-acetyllysine; alternateBy similarity
Cross-linki92 – 92Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternateBy similarity

Post-translational modificationi

Acetylation at Lys-6 (H4K5ac), Lys-9 (H4K8ac), Lys-13 (H4K12ac) and Lys-17 (H4K16ac) occurs in coding regions of the genome but not in heterochromatin.By similarity
Citrullination at Arg-4 (H4R3ci) by PADI4 impairs methylation.By similarity
Monomethylation and asymmetric dimethylation at Arg-4 (H4R3me1 and H4R3me2a, respectively) by PRMT1 favors acetylation at Lys-9 (H4K8ac) and Lys-13 (H4K12ac). Demethylation is performed by JMJD6. Symmetric dimethylation on Arg-4 (H4R3me2s) by the PRDM1/PRMT5 complex may play a crucial role in the germ-cell lineage (By similarity).By similarity
Monomethylated, dimethylated or trimethylated at Lys-21 (H4K20me1, H4K20me2, H4K20me3). Monomethylation is performed by SET8. Trimethylation is performed by SUV420H1 and SUV420H2 and induces gene silencing (By similarity).By similarity
Phosphorylated by PAK2 at Ser-48 (H4S47ph). This phosphorylation increases the association of H3.3-H4 with the histone chaperone HIRA, thus promoting nucleosome assembly of H3.3-H4 and inhibiting nucleosome assembly of H3.1-H4 (By similarity).By similarity
Ubiquitinated by the CUL4-DDB-RBX1 complex in response to ultraviolet irradiation. This may weaken the interaction between histones and DNA and facilitate DNA accessibility to repair proteins. Monoubiquitinated at Lys-92 of histone H4 (H4K91ub1) in response to DNA damage. The exact role of H4K91ub1 in DNA damage response is still unclear but it may function as a licensing signal for additional histone H4 post-translational modifications such as H4 Lys-21 methylation (H4K20me) (By similarity).By similarity
Sumoylated, which is associated with transcriptional repression.By similarity

Keywords - PTMi

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

Proteomic databases

PaxDbiP62801.
PRIDEiP62801.

Expressioni

Gene expression databases

ExpressionAtlasiP62801. baseline and differential.

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

BioGridi679227. 7 interactions.
IntActiP62801. 2 interactions.
STRINGi9031.ENSGALP00000037292.

Structurei

Secondary structure

1
103
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi26 – 294Combined sources
Helixi32 – 4110Combined sources
Helixi51 – 7626Combined sources
Beta strandi80 – 823Combined sources
Helixi84 – 9310Combined sources
Beta strandi97 – 1004Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EQZX-ray2.50D/H1-103[»]
1HIOX-ray3.10D28-103[»]
1HQ3X-ray2.15D/H1-103[»]
1TZYX-ray1.90D/H1-103[»]
2AROX-ray2.10D/H1-103[»]
2HIOX-ray3.10D1-103[»]
3C9Kelectron microscopy20.00D/H2-103[»]
ProteinModelPortaliP62801.
SMRiP62801. Positions 21-102.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP62801.

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H4 family.Curated

Phylogenomic databases

eggNOGiCOG2036.
GeneTreeiENSGT00760000119019.
HOVERGENiHBG051878.
InParanoidiP62801.
KOiK11254.
OMAiSTHNERI.
PhylomeDBiP62801.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR001951. Histone_H4.
IPR019809. Histone_H4_CS.
[Graphical view]
PfamiPF00125. Histone. 1 hit.
[Graphical view]
PRINTSiPR00623. HISTONEH4.
SMARTiSM00417. H4. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00047. HISTONE_H4. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P62801-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL
60 70 80 90 100
IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG

FGG
Length:103
Mass (Da):11,367
Last modified:January 23, 2007 - v2
Checksum:iA9E5DFD3F8B97598
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02218 Genomic DNA. Translation: CAA26137.1.
X02218 Genomic DNA. Translation: CAA26140.1.
J00866 Genomic DNA. No translation available.
M74533 Genomic DNA. Translation: AAA73091.1.
M74534 Genomic DNA. Translation: AAA73092.1.
U37575 Genomic DNA. Translation: AAC59999.1.
U37575 Genomic DNA. Translation: AAC60001.1.
PIRiA02640. HSCH4.
JH0507.
RefSeqiNP_001032932.1. NM_001037843.1.
NP_001032934.1. NM_001037845.1.
NP_001268414.1. NM_001281485.1.
XP_001233095.1. XM_001233094.3.
XP_001233180.1. XM_001233179.3.
XP_003640418.1. XM_003640370.2.
XP_004937726.1. XM_004937669.1.
XP_425458.2. XM_425458.4.
UniGeneiGga.39882.

Genome annotation databases

EnsembliENSGALT00000046233; ENSGALP00000041526; ENSGALG00000025786.
GeneIDi100858049.
100858319.
417946.
417950.
427884.
770005.
770079.
770142.
KEGGigga:100858049.
gga:100858319.
gga:417946.
gga:417950.
gga:427884.
gga:770005.
gga:770079.
gga:770142.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02218 Genomic DNA. Translation: CAA26137.1.
X02218 Genomic DNA. Translation: CAA26140.1.
J00866 Genomic DNA. No translation available.
M74533 Genomic DNA. Translation: AAA73091.1.
M74534 Genomic DNA. Translation: AAA73092.1.
U37575 Genomic DNA. Translation: AAC59999.1.
U37575 Genomic DNA. Translation: AAC60001.1.
PIRiA02640. HSCH4.
JH0507.
RefSeqiNP_001032932.1. NM_001037843.1.
NP_001032934.1. NM_001037845.1.
NP_001268414.1. NM_001281485.1.
XP_001233095.1. XM_001233094.3.
XP_001233180.1. XM_001233179.3.
XP_003640418.1. XM_003640370.2.
XP_004937726.1. XM_004937669.1.
XP_425458.2. XM_425458.4.
UniGeneiGga.39882.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EQZX-ray2.50D/H1-103[»]
1HIOX-ray3.10D28-103[»]
1HQ3X-ray2.15D/H1-103[»]
1TZYX-ray1.90D/H1-103[»]
2AROX-ray2.10D/H1-103[»]
2HIOX-ray3.10D1-103[»]
3C9Kelectron microscopy20.00D/H2-103[»]
ProteinModelPortaliP62801.
SMRiP62801. Positions 21-102.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi679227. 7 interactions.
IntActiP62801. 2 interactions.
STRINGi9031.ENSGALP00000037292.

Chemistry

BindingDBiP62801.

Proteomic databases

PaxDbiP62801.
PRIDEiP62801.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSGALT00000046233; ENSGALP00000041526; ENSGALG00000025786.
GeneIDi100858049.
100858319.
417946.
417950.
427884.
770005.
770079.
770142.
KEGGigga:100858049.
gga:100858319.
gga:417946.
gga:417950.
gga:427884.
gga:770005.
gga:770079.
gga:770142.

Organism-specific databases

CTDi100858049.
100858319.
417946.
554313.
770079.
770142.
8359.
8360.

Phylogenomic databases

eggNOGiCOG2036.
GeneTreeiENSGT00760000119019.
HOVERGENiHBG051878.
InParanoidiP62801.
KOiK11254.
OMAiSTHNERI.
PhylomeDBiP62801.

Enzyme and pathway databases

ReactomeiREACT_275071. HATs acetylate histones.
REACT_276260. DNA methylation.
REACT_277792. RNA Polymerase I Chain Elongation.
REACT_286644. Meiotic recombination.
REACT_299305. PRC2 methylates histones and DNA.
REACT_299693. PKMTs methylate histone lysines.
REACT_310543. RMTs methylate histone arginines.
REACT_316866. Transcriptional regulation by small RNAs.
REACT_316940. SIRT1 negatively regulates rRNA Expression.
REACT_322027. RNA Polymerase I Promoter Opening.
REACT_334370. Condensation of Prophase Chromosomes.
REACT_339698. Deposition of new CENPA-containing nucleosomes at the centromere.
REACT_340836. NoRC negatively regulates rRNA expression.
REACT_342239. Senescence-Associated Secretory Phenotype (SASP).
REACT_348443. Oxidative Stress Induced Senescence.

Miscellaneous databases

EvolutionaryTraceiP62801.
NextBioi20821175.
PROiP62801.

Gene expression databases

ExpressionAtlasiP62801. baseline and differential.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR001951. Histone_H4.
IPR019809. Histone_H4_CS.
[Graphical view]
PfamiPF00125. Histone. 1 hit.
[Graphical view]
PRINTSiPR00623. HISTONEH4.
SMARTiSM00417. H4. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00047. HISTONE_H4. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Inverted duplication of histone genes in chicken and disposition of regulatory sequences."
    Wang S.W., Robins A.J., D'Andrea R., Wells J.R.E.
    Nucleic Acids Res. 13:1369-1387(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Genomic organization, DNA sequence, and expression of chicken embryonic histone genes."
    Sugarman B.J., Dodgson J.B., Engel J.D.
    J. Biol. Chem. 258:9005-9016(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "Nucleotide sequences of two members of the chicken H4 histone-encoding gene family."
    Nakayama T., Takechi S., Ohshige T., Kondo K., Yamamoto K.
    Gene 108:311-312(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (H4-III AND H4-IV).
  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] (H4-VI AND H4-VII).
    Strain: White leghorn.
    Tissue: Liver.
  5. "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).
  6. "Asymmetries in the nucleosome core particle at 2.5 A resolution."
    Harp J.M., Hanson B.L., Timm D.E., Bunick G.J.
    Acta Crystallogr. D 56:1513-1534(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).

Entry informationi

Entry nameiH4_CHICK
AccessioniPrimary (citable) accession number: P62801
Secondary accession number(s): P02304, P02305
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: July 22, 2015
This is version 108 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, 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.