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Protein

Histone H4

Gene
N/A
Organism
Xenopus laevis (African clawed frog)
Status
Reviewed-Annotation score: Annotation score: 4 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

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H4
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-6493984. hist1h4a.

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 – 103102Histone H4PRO_0000158376Add
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 KMT5B and KMT5C 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

PRIDEiP62799.

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.

Binary interactionsi

WithEntry#Exp.IntActNotes
P842332EBI-302085,EBI-350041

Protein-protein interaction databases

BioGridi104647. 11 interactions.
DIPiDIP-37429N.
IntActiP62799. 4 interactions.

Structurei

Secondary structure

1
103
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 127Combined sources
Beta strandi13 – 175Combined sources
Helixi23 – 264Combined sources
Helixi27 – 293Combined sources
Helixi32 – 4110Combined sources
Beta strandi45 – 473Combined sources
Helixi51 – 7626Combined sources
Beta strandi80 – 823Combined sources
Helixi84 – 907Combined sources
Turni91 – 944Combined sources
Beta strandi96 – 1005Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AOIX-ray2.80B/F17-103[»]
1KX3X-ray2.00B/F2-103[»]
1KX4X-ray2.60B/F2-103[»]
1KX5X-ray1.94B/F2-103[»]
1M18X-ray2.45B/F2-103[»]
1M19X-ray2.30B/F2-103[»]
1M1AX-ray2.65B/F2-103[»]
1P34X-ray2.70B/F2-103[»]
1P3AX-ray3.00B/F2-103[»]
1P3BX-ray3.00B/F2-103[»]
1P3FX-ray2.90B/F2-103[»]
1P3GX-ray2.70B/F2-103[»]
1P3IX-ray2.30B/F2-103[»]
1P3KX-ray2.90B/F2-103[»]
1P3LX-ray2.40B/F2-103[»]
1P3MX-ray2.90B/F2-103[»]
1P3OX-ray2.75B/F2-103[»]
1P3PX-ray2.70B/F2-103[»]
1S32X-ray2.05B/F2-103[»]
1ZBBX-ray9.00B/F/b/f2-103[»]
1ZLAX-ray2.90B/F2-103[»]
2F8NX-ray2.90B/F1-103[»]
2FJ7X-ray3.20B/F2-103[»]
2HUEX-ray1.70C21-103[»]
2IO5X-ray2.70C2-103[»]
2NZDX-ray2.65B/F2-103[»]
3B6FX-ray3.45B/F2-103[»]
3B6GX-ray3.45B/F2-103[»]
3C1BX-ray2.20B/F2-103[»]
3C1CX-ray3.15B/F2-103[»]
3KUYX-ray2.90B/F2-103[»]
3KWQX-ray3.50B/F21-103[»]
3KXBX-ray3.20B/F2-103[»]
3LELX-ray2.95B/F/L/P2-103[»]
3LJAX-ray2.75B/F2-103[»]
3LZ0X-ray2.50B/F2-103[»]
3LZ1X-ray2.50B/F2-103[»]
3MGPX-ray2.44B/F2-103[»]
3MGQX-ray2.65B/F2-103[»]
3MGRX-ray2.30B/F2-103[»]
3MGSX-ray3.15B/F2-103[»]
3MNNX-ray2.50B/F2-103[»]
3MVDX-ray2.90B/F2-103[»]
3O62X-ray3.22B/F2-103[»]
3REHX-ray2.50B/F2-103[»]
3REIX-ray2.65B/F2-103[»]
3REJX-ray2.55B/F2-103[»]
3REKX-ray2.60B/F2-103[»]
3RELX-ray2.70B/F2-103[»]
3TU4X-ray3.00B/F2-103[»]
3UT9X-ray2.20B/F2-103[»]
3UTAX-ray2.07B/F2-103[»]
3UTBX-ray2.20B/F2-103[»]
4EO5X-ray2.35C21-103[»]
4J8UX-ray2.38B/F2-103[»]
4J8VX-ray2.58B/F2-103[»]
4J8WX-ray2.41B/F2-103[»]
4J8XX-ray2.87B/F2-103[»]
4KGCX-ray2.69B/F1-103[»]
4LD9X-ray3.31B/F1-103[»]
4R8PX-ray3.28B/F2-103[»]
4WU8X-ray2.45B/F2-103[»]
4WU9X-ray2.60B/F2-103[»]
4XUJX-ray3.18B/F2-103[»]
4XZQX-ray2.40B/F25-103[»]
4YS3X-ray3.00B/F25-103[»]
4Z66X-ray2.50B/F22-103[»]
4ZBJX-ray2.25C21-103[»]
4ZUXX-ray3.82B/F/L/P1-103[»]
5BS7X-ray3.30C/D2-103[»]
5BSAX-ray4.61C/D2-103[»]
5CP6X-ray2.60B/F2-103[»]
5E5AX-ray2.81B/F1-103[»]
5F99X-ray2.63B/F1-103[»]
5HQ2X-ray4.50B2-103[»]
ProteinModelPortaliP62799.
SMRiP62799. Positions 21-102.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP62799.

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H4 family.Curated

Phylogenomic databases

HOVERGENiHBG051878.
KOiK11254.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR001951. Histone_H4.
IPR019809. Histone_H4_CS.
IPR004823. TAF_TATA-bd.
[Graphical view]
PRINTSiPR00623. HISTONEH4.
SMARTiSM00417. H4. 1 hit.
SM00803. TAF. 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.

P62799-1 [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
X00224 Genomic DNA. Translation: CAA25042.1.
X03017 Genomic DNA. Translation: CAA26809.1.
X03017 Genomic DNA. Translation: CAA26814.1.
X03018 Genomic DNA. Translation: CAA26819.1.
M21286 Genomic DNA. Translation: AAA49761.1.
M21286 Genomic DNA. Translation: AAA49766.1.
M21287 Genomic DNA. Translation: AAA49771.1.
BC078038 mRNA. Translation: AAH78038.1.
PIRiA02641. HSXL4.
RefSeqiNP_001087926.1. NM_001094457.1.
UniGeneiXl.85592.

Genome annotation databases

GeneIDi447787.
KEGGixla:447787.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X00224 Genomic DNA. Translation: CAA25042.1.
X03017 Genomic DNA. Translation: CAA26809.1.
X03017 Genomic DNA. Translation: CAA26814.1.
X03018 Genomic DNA. Translation: CAA26819.1.
M21286 Genomic DNA. Translation: AAA49761.1.
M21286 Genomic DNA. Translation: AAA49766.1.
M21287 Genomic DNA. Translation: AAA49771.1.
BC078038 mRNA. Translation: AAH78038.1.
PIRiA02641. HSXL4.
RefSeqiNP_001087926.1. NM_001094457.1.
UniGeneiXl.85592.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AOIX-ray2.80B/F17-103[»]
1KX3X-ray2.00B/F2-103[»]
1KX4X-ray2.60B/F2-103[»]
1KX5X-ray1.94B/F2-103[»]
1M18X-ray2.45B/F2-103[»]
1M19X-ray2.30B/F2-103[»]
1M1AX-ray2.65B/F2-103[»]
1P34X-ray2.70B/F2-103[»]
1P3AX-ray3.00B/F2-103[»]
1P3BX-ray3.00B/F2-103[»]
1P3FX-ray2.90B/F2-103[»]
1P3GX-ray2.70B/F2-103[»]
1P3IX-ray2.30B/F2-103[»]
1P3KX-ray2.90B/F2-103[»]
1P3LX-ray2.40B/F2-103[»]
1P3MX-ray2.90B/F2-103[»]
1P3OX-ray2.75B/F2-103[»]
1P3PX-ray2.70B/F2-103[»]
1S32X-ray2.05B/F2-103[»]
1ZBBX-ray9.00B/F/b/f2-103[»]
1ZLAX-ray2.90B/F2-103[»]
2F8NX-ray2.90B/F1-103[»]
2FJ7X-ray3.20B/F2-103[»]
2HUEX-ray1.70C21-103[»]
2IO5X-ray2.70C2-103[»]
2NZDX-ray2.65B/F2-103[»]
3B6FX-ray3.45B/F2-103[»]
3B6GX-ray3.45B/F2-103[»]
3C1BX-ray2.20B/F2-103[»]
3C1CX-ray3.15B/F2-103[»]
3KUYX-ray2.90B/F2-103[»]
3KWQX-ray3.50B/F21-103[»]
3KXBX-ray3.20B/F2-103[»]
3LELX-ray2.95B/F/L/P2-103[»]
3LJAX-ray2.75B/F2-103[»]
3LZ0X-ray2.50B/F2-103[»]
3LZ1X-ray2.50B/F2-103[»]
3MGPX-ray2.44B/F2-103[»]
3MGQX-ray2.65B/F2-103[»]
3MGRX-ray2.30B/F2-103[»]
3MGSX-ray3.15B/F2-103[»]
3MNNX-ray2.50B/F2-103[»]
3MVDX-ray2.90B/F2-103[»]
3O62X-ray3.22B/F2-103[»]
3REHX-ray2.50B/F2-103[»]
3REIX-ray2.65B/F2-103[»]
3REJX-ray2.55B/F2-103[»]
3REKX-ray2.60B/F2-103[»]
3RELX-ray2.70B/F2-103[»]
3TU4X-ray3.00B/F2-103[»]
3UT9X-ray2.20B/F2-103[»]
3UTAX-ray2.07B/F2-103[»]
3UTBX-ray2.20B/F2-103[»]
4EO5X-ray2.35C21-103[»]
4J8UX-ray2.38B/F2-103[»]
4J8VX-ray2.58B/F2-103[»]
4J8WX-ray2.41B/F2-103[»]
4J8XX-ray2.87B/F2-103[»]
4KGCX-ray2.69B/F1-103[»]
4LD9X-ray3.31B/F1-103[»]
4R8PX-ray3.28B/F2-103[»]
4WU8X-ray2.45B/F2-103[»]
4WU9X-ray2.60B/F2-103[»]
4XUJX-ray3.18B/F2-103[»]
4XZQX-ray2.40B/F25-103[»]
4YS3X-ray3.00B/F25-103[»]
4Z66X-ray2.50B/F22-103[»]
4ZBJX-ray2.25C21-103[»]
4ZUXX-ray3.82B/F/L/P1-103[»]
5BS7X-ray3.30C/D2-103[»]
5BSAX-ray4.61C/D2-103[»]
5CP6X-ray2.60B/F2-103[»]
5E5AX-ray2.81B/F1-103[»]
5F99X-ray2.63B/F1-103[»]
5HQ2X-ray4.50B2-103[»]
ProteinModelPortaliP62799.
SMRiP62799. Positions 21-102.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi104647. 11 interactions.
DIPiDIP-37429N.
IntActiP62799. 4 interactions.

Proteomic databases

PRIDEiP62799.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi447787.
KEGGixla:447787.

Organism-specific databases

CTDi8359.
XenbaseiXB-GENE-6493984. hist1h4a.

Phylogenomic databases

HOVERGENiHBG051878.
KOiK11254.

Miscellaneous databases

EvolutionaryTraceiP62799.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR001951. Histone_H4.
IPR019809. Histone_H4_CS.
IPR004823. TAF_TATA-bd.
[Graphical view]
PRINTSiPR00623. HISTONEH4.
SMARTiSM00417. H4. 1 hit.
SM00803. TAF. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00047. HISTONE_H4. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiH4_XENLA
AccessioniPrimary (citable) accession number: P62799
Secondary accession number(s): P02304, P02305, Q6AZG5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: September 7, 2016
This is version 113 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

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.