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Protein

Histone H4

Gene

Hist1h4b

more
Organism
Rattus norvegicus (Rat)
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.
Osteogenic growth peptide (OGP) stimulates osteogenesis and hematopoiesis.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi17 – 215

GO - Molecular functioni

  • DNA binding Source: RGD
  • poly(A) RNA binding Source: Ensembl

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Differentiation, Osteogenesis

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiR-RNO-201722. Formation of the beta-catenin:TCF transactivating complex.
R-RNO-212300. PRC2 methylates histones and DNA.
R-RNO-2299718. Condensation of Prophase Chromosomes.
R-RNO-2559580. Oxidative Stress Induced Senescence.
R-RNO-2559582. Senescence-Associated Secretory Phenotype (SASP).
R-RNO-2559586. DNA Damage/Telomere Stress Induced Senescence.
R-RNO-3214841. PKMTs methylate histone lysines.
R-RNO-3214842. HDMs demethylate histones.
R-RNO-3214847. HATs acetylate histones.
R-RNO-3214858. RMTs methylate histone arginines.
R-RNO-427359. SIRT1 negatively regulates rRNA Expression.
R-RNO-427413. NoRC negatively regulates rRNA expression.
R-RNO-5250924. B-WICH complex positively regulates rRNA expression.
R-RNO-5578749. Transcriptional regulation by small RNAs.
R-RNO-5625886. Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3.
R-RNO-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
R-RNO-5693571. Nonhomologous End-Joining (NHEJ).
R-RNO-606279. Deposition of new CENPA-containing nucleosomes at the centromere.
R-RNO-69473. G2/M DNA damage checkpoint.
R-RNO-73728. RNA Polymerase I Promoter Opening.
R-RNO-73777. RNA Polymerase I Chain Elongation.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H4
Cleaved into the following chain:
Gene namesi
Name:Hist1h4b
Synonyms:Hist4
AND
Name:Hist1h4m
AND
Name:Hist4h4
Synonyms:H4ft
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componentsi: Chromosome 17, Chromosome 2, Chromosome 4

Organism-specific databases

RGDi620814. Hist1h4b.

Subcellular locationi

  • Nucleus 1 Publication
  • Chromosome 1 Publication

  • Note: Osteogenic growth peptide is secreted by a mechanism independent from a hydrophobic signal sequence. The mature peptide may be imported into secretory lysosomes by an ABCA1-related protein.

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001583552 – 103Histone H4Add BLAST102
PeptideiPRO_000022559190 – 103Osteogenic growth peptideAdd BLAST14

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserine1 Publication1
Modified residuei2PhosphoserineBy similarity1
Modified residuei4Asymmetric dimethylarginine; by PRMT1; alternateBy similarity1
Modified residuei4Citrulline; alternateBy similarity1
Modified residuei4Omega-N-methylarginine; by PRMT1; alternateBy similarity1
Modified residuei4Symmetric dimethylarginine; by PRMT5 and PRMT7; alternateBy similarity1
Modified residuei6N6-acetyllysine; alternateBy similarity1
Modified residuei6N6-crotonyllysine; alternateBy similarity1
Modified residuei9N6-acetyllysine; alternateBy similarity1
Modified residuei9N6-crotonyllysine; alternateBy similarity1
Modified residuei13N6-acetyllysine; alternateBy similarity1
Modified residuei13N6-crotonyllysine; alternateBy similarity1
Cross-linki13Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateBy similarity
Modified residuei17N6-acetyllysine; alternate1 Publication1
Modified residuei17N6-crotonyllysine; alternateBy similarity1
Modified residuei21N6,N6,N6-trimethyllysine; alternateBy similarity1
Modified residuei21N6,N6-dimethyllysine; alternate1 Publication1
Modified residuei21N6-methyllysine; alternate1 Publication1
Modified residuei32N6-acetyllysineBy similarity1
Modified residuei48PhosphoserineCombined sources1
Modified residuei52PhosphotyrosineBy similarity1
Modified residuei81PhosphothreonineCombined sources1
Modified residuei89PhosphotyrosineCombined sources1
Modified residuei92N6-acetyllysine; alternateBy similarity1
Modified residuei92N6-succinyllysine; alternateBy similarity1
Cross-linki92Glycyl 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
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 (By similarity).By similarity

Keywords - PTMi

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

Proteomic databases

PaxDbiP62804.
PRIDEiP62804.

PTM databases

iPTMnetiP62804.
PhosphoSitePlusiP62804.
SwissPalmiP62804.

Expressioni

Tissue specificityi

OGP is found in serum. A potentially OGP-specific transcript is highly expressed in spleen with lower levels in lung, liver, thymus, spinal chord, pituitary gland, adrenal gland, bone marrow and lymph nodes as well as very low levels in kidney, heart and brain.1 Publication

Gene expression databases

BgeeiENSRNOG00000030142.
GenevisibleiP62804. RN.

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

BioGridi1200084. 1 interactor.
249165. 4 interactors.
595036. 1 interactor.
STRINGi10116.ENSRNOP00000067813.

Structurei

3D structure databases

ProteinModelPortaliP62804.
SMRiP62804.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H4 family.Curated

Phylogenomic databases

eggNOGiKOG3467. Eukaryota.
COG2036. LUCA.
GeneTreeiENSGT00760000119019.
HOGENOMiHOG000234654.
HOVERGENiHBG051878.
InParanoidiP62804.
KOiK11251.
K11254.
OMAiSTHNERI.
OrthoDBiEOG091G0XGD.
PhylomeDBiP62804.

Family and domain databases

CDDicd00076. H4. 1 hit.
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]

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by alternative initiation. AlignAdd to basket

Isoform Histone H4 (identifier: P62804-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« 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
Isoform OGP precursor (identifier: P62804-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-84: Missing.

Show »
Length:19
Mass (Da):2,131
Checksum:iDA46847BA27B7A8B
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0188041 – 84Missing in isoform OGP precursor. CuratedAdd BLAST84

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M27433 Genomic DNA. Translation: AAA60735.1.
X13554 Genomic DNA. Translation: CAA31906.1.
M28409 Genomic DNA. Translation: AAA41306.1.
AY936209 mRNA. Translation: AAX28930.1.
BC100619 mRNA. Translation: AAI00620.1.
PIRiA91265. HSRT4.
S53749.
RefSeqiNP_001116941.1. NM_001123469.1. [P62804-1]
NP_001258150.1. NM_001271221.1. [P62804-1]
NP_073177.1. NM_022686.2. [P62804-1]
XP_003749904.3. XM_003749856.4. [P62804-1]
XP_008761668.1. XM_008763446.1. [P62804-1]
XP_008761670.1. XM_008763448.2. [P62804-1]
XP_008769992.1. XM_008771770.2. [P62804-1]
XP_008772221.1. XM_008773999.1. [P62804-1]
XP_578415.4. XM_578415.6. [P62804-1]
UniGeneiRn.10465.
Rn.1659.
Rn.220155.
Rn.234305.

Genome annotation databases

EnsembliENSRNOT00000040210; ENSRNOP00000039602; ENSRNOG00000032224. [P62804-1]
ENSRNOT00000071512; ENSRNOP00000065233; ENSRNOG00000045840. [P62804-1]
ENSRNOT00000072147; ENSRNOP00000066653; ENSRNOG00000048735. [P62804-1]
ENSRNOT00000072286; ENSRNOP00000067502; ENSRNOG00000050933. [P62804-1]
ENSRNOT00000074109; ENSRNOP00000066622; ENSRNOG00000046636. [P62804-1]
ENSRNOT00000074198; ENSRNOP00000066695; ENSRNOG00000048642. [P62804-1]
ENSRNOT00000074526; ENSRNOP00000067813; ENSRNOG00000045978. [P62804-1]
ENSRNOT00000075065; ENSRNOP00000067176; ENSRNOG00000048215. [P62804-1]
ENSRNOT00000080490; ENSRNOP00000071163; ENSRNOG00000054017. [P62804-1]
ENSRNOT00000085381; ENSRNOP00000069989; ENSRNOG00000058444. [P62804-1]
ENSRNOT00000088408; ENSRNOP00000074659; ENSRNOG00000051891. [P62804-1]
ENSRNOT00000091201; ENSRNOP00000074796; ENSRNOG00000057690. [P62804-1]
GeneIDi100912489.
100912564.
291152.
295277.
364723.
500351.
502913.
64627.
KEGGirno:100360950.
rno:100912489.
rno:102548682.
rno:102551184.
rno:102557184.
rno:291152.
rno:295277.
rno:364723.
rno:500351.
rno:64627.
rno:679983.
rno:680097.
UCSCiRGD:620814. rat. [P62804-1]

Keywords - Coding sequence diversityi

Alternative initiation

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M27433 Genomic DNA. Translation: AAA60735.1.
X13554 Genomic DNA. Translation: CAA31906.1.
M28409 Genomic DNA. Translation: AAA41306.1.
AY936209 mRNA. Translation: AAX28930.1.
BC100619 mRNA. Translation: AAI00620.1.
PIRiA91265. HSRT4.
S53749.
RefSeqiNP_001116941.1. NM_001123469.1. [P62804-1]
NP_001258150.1. NM_001271221.1. [P62804-1]
NP_073177.1. NM_022686.2. [P62804-1]
XP_003749904.3. XM_003749856.4. [P62804-1]
XP_008761668.1. XM_008763446.1. [P62804-1]
XP_008761670.1. XM_008763448.2. [P62804-1]
XP_008769992.1. XM_008771770.2. [P62804-1]
XP_008772221.1. XM_008773999.1. [P62804-1]
XP_578415.4. XM_578415.6. [P62804-1]
UniGeneiRn.10465.
Rn.1659.
Rn.220155.
Rn.234305.

3D structure databases

ProteinModelPortaliP62804.
SMRiP62804.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi1200084. 1 interactor.
249165. 4 interactors.
595036. 1 interactor.
STRINGi10116.ENSRNOP00000067813.

PTM databases

iPTMnetiP62804.
PhosphoSitePlusiP62804.
SwissPalmiP62804.

Proteomic databases

PaxDbiP62804.
PRIDEiP62804.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000040210; ENSRNOP00000039602; ENSRNOG00000032224. [P62804-1]
ENSRNOT00000071512; ENSRNOP00000065233; ENSRNOG00000045840. [P62804-1]
ENSRNOT00000072147; ENSRNOP00000066653; ENSRNOG00000048735. [P62804-1]
ENSRNOT00000072286; ENSRNOP00000067502; ENSRNOG00000050933. [P62804-1]
ENSRNOT00000074109; ENSRNOP00000066622; ENSRNOG00000046636. [P62804-1]
ENSRNOT00000074198; ENSRNOP00000066695; ENSRNOG00000048642. [P62804-1]
ENSRNOT00000074526; ENSRNOP00000067813; ENSRNOG00000045978. [P62804-1]
ENSRNOT00000075065; ENSRNOP00000067176; ENSRNOG00000048215. [P62804-1]
ENSRNOT00000080490; ENSRNOP00000071163; ENSRNOG00000054017. [P62804-1]
ENSRNOT00000085381; ENSRNOP00000069989; ENSRNOG00000058444. [P62804-1]
ENSRNOT00000088408; ENSRNOP00000074659; ENSRNOG00000051891. [P62804-1]
ENSRNOT00000091201; ENSRNOP00000074796; ENSRNOG00000057690. [P62804-1]
GeneIDi100912489.
100912564.
291152.
295277.
364723.
500351.
502913.
64627.
KEGGirno:100360950.
rno:100912489.
rno:102548682.
rno:102551184.
rno:102557184.
rno:291152.
rno:295277.
rno:364723.
rno:500351.
rno:64627.
rno:679983.
rno:680097.
UCSCiRGD:620814. rat. [P62804-1]

Organism-specific databases

CTDi100041230.
121504.
500351.
665433.
8359.
8366.
97122.
RGDi620814. Hist1h4b.

Phylogenomic databases

eggNOGiKOG3467. Eukaryota.
COG2036. LUCA.
GeneTreeiENSGT00760000119019.
HOGENOMiHOG000234654.
HOVERGENiHBG051878.
InParanoidiP62804.
KOiK11251.
K11254.
OMAiSTHNERI.
OrthoDBiEOG091G0XGD.
PhylomeDBiP62804.

Enzyme and pathway databases

ReactomeiR-RNO-201722. Formation of the beta-catenin:TCF transactivating complex.
R-RNO-212300. PRC2 methylates histones and DNA.
R-RNO-2299718. Condensation of Prophase Chromosomes.
R-RNO-2559580. Oxidative Stress Induced Senescence.
R-RNO-2559582. Senescence-Associated Secretory Phenotype (SASP).
R-RNO-2559586. DNA Damage/Telomere Stress Induced Senescence.
R-RNO-3214841. PKMTs methylate histone lysines.
R-RNO-3214842. HDMs demethylate histones.
R-RNO-3214847. HATs acetylate histones.
R-RNO-3214858. RMTs methylate histone arginines.
R-RNO-427359. SIRT1 negatively regulates rRNA Expression.
R-RNO-427413. NoRC negatively regulates rRNA expression.
R-RNO-5250924. B-WICH complex positively regulates rRNA expression.
R-RNO-5578749. Transcriptional regulation by small RNAs.
R-RNO-5625886. Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3.
R-RNO-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
R-RNO-5693571. Nonhomologous End-Joining (NHEJ).
R-RNO-606279. Deposition of new CENPA-containing nucleosomes at the centromere.
R-RNO-69473. G2/M DNA damage checkpoint.
R-RNO-73728. RNA Polymerase I Promoter Opening.
R-RNO-73777. RNA Polymerase I Chain Elongation.

Miscellaneous databases

PROiP62804.

Gene expression databases

BgeeiENSRNOG00000030142.
GenevisibleiP62804. RN.

Family and domain databases

CDDicd00076. H4. 1 hit.
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_RAT
AccessioniPrimary (citable) accession number: P62804
Secondary accession number(s): P02304
, P02305, Q5BM23, Q7M0E8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: November 30, 2016
This is version 128 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

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. 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.