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Protein

Histone H3.3

Gene

h3f3a

more
Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: -Experimental evidence at transcript leveli

Functioni

Variant histone H3 which replaces conventional H3 in a wide range of nucleosomes in active genes. Constitutes the predominant form of histone H3 in non-dividing cells and is incorporated into chromatin independently of DNA synthesis. Deposited at sites of nucleosomal displacement throughout transcribed genes, suggesting that it represents an epigenetic imprint of transcriptionally active chromatin. 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.By similarity

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding

Enzyme and pathway databases

ReactomeiR-DRE-212300 PRC2 methylates histones and DNA
R-DRE-2299718 Condensation of Prophase Chromosomes
R-DRE-5689901 Metalloprotease DUBs
R-DRE-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-DRE-983231 Factors involved in megakaryocyte development and platelet production

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H3.3
Gene namesi
Name:h3f3a
ORF Names:zgc:56193, zgc:86731
AND
Name:h3f3b.1
ORF Names:zgc:110292
AND
Name:h3f3c
ORF Names:zgc:64222
AND
Name:h3f3d
ORF Names:zgc:56418
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
Proteomesi
  • UP000000437 Componentsi: Chromosome 15, Chromosome 24, Chromosome 3, Chromosome 5

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCurated
ChainiPRO_00002539562 – 136Histone H3.3Add BLAST135

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei3Asymmetric dimethylarginine; by PRMT6By similarity1
Modified residuei4Phosphothreonine; by HASPINBy similarity1
Modified residuei5Allysine; alternateBy similarity1
Modified residuei5N6,N6,N6-trimethyllysine; alternateBy similarity1
Modified residuei5N6,N6-dimethyllysine; alternateBy similarity1
Modified residuei5N6-(2-hydroxyisobutyryl)lysine; alternateBy similarity1
Modified residuei5N6-acetyllysine; alternateBy similarity1
Modified residuei5N6-methyllysine; alternateBy similarity1
Modified residuei7Phosphothreonine; by PKCBy similarity1
Modified residuei10N6-(2-hydroxyisobutyryl)lysine; alternateBy similarity1
Modified residuei10N6-methylated lysineBy similarity1
Modified residuei11ADP-ribosylserine; alternateBy similarity1
Modified residuei11Phosphoserine; alternate; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5By similarity1
Modified residuei12Phosphothreonine; by PKCBy similarity1
Modified residuei15N6-(2-hydroxyisobutyryl)lysine; alternateBy similarity1
Modified residuei15N6-acetyllysineBy similarity1
Modified residuei18Asymmetric dimethylarginineBy similarity1
Modified residuei19N6-(2-hydroxyisobutyryl)lysine; alternateBy similarity1
Modified residuei19N6-acetyllysine; alternateBy similarity1
Modified residuei19N6-butyryllysine; alternateBy similarity1
Modified residuei19N6-methylated lysine; alternateBy similarity1
Modified residuei24N6-(2-hydroxyisobutyryl)lysine; alternateBy similarity1
Modified residuei24N6-acetyllysineBy similarity1
Modified residuei24N6-butyryllysine; alternateBy similarity1
Modified residuei28N6-(2-hydroxyisobutyryl)lysine; alternateBy similarity1
Modified residuei28N6-acetyllysine; alternateBy similarity1
Modified residuei28N6-methylated lysine; alternateBy similarity1
Modified residuei29ADP-ribosylserine; alternateBy similarity1
Modified residuei29Phosphoserine; alternate; by AURKB, AURKC and RPS6KA5By similarity1
Modified residuei37N6-(2-hydroxyisobutyryl)lysine; alternateBy similarity1
Modified residuei37N6-acetyllysine; alternateBy similarity1
Modified residuei37N6-methylated lysine; alternateBy similarity1
Modified residuei42PhosphotyrosineBy similarity1
Modified residuei57N6-(2-hydroxyisobutyryl)lysine; alternateBy similarity1
Modified residuei57N6-succinyllysine; alternateBy similarity1
Modified residuei58PhosphoserineBy similarity1
Modified residuei65N6-(2-hydroxyisobutyryl)lysine; alternateBy similarity1
Modified residuei65N6-methylated lysineBy similarity1
Modified residuei80N6-(2-hydroxyisobutyryl)lysine; alternateBy similarity1
Modified residuei80N6-methylated lysineBy similarity1
Modified residuei80N6-succinyllysine; alternateBy similarity1
Modified residuei81PhosphothreonineBy similarity1
Modified residuei116N6-acetyllysineBy similarity1
Modified residuei123N6-(2-hydroxyisobutyryl)lysine; alternateBy similarity1
Modified residuei123N6-acetyllysine; alternateBy similarity1
Modified residuei123N6-methyllysine; alternateBy similarity1

Post-translational modificationi

Acetylation is generally linked to gene activation. Acetylation on Lys-19 (H3K18ac) and Lys-24 (H3K24ac) favors methylation at Arg-18 (H3R17me). Acetylation at Lys-123 (H3K122ac) by EP300/p300 plays a central role in chromatin structure: localizes at the surface of the histone octamer and stimulates transcription, possibly by promoting nucleosome instability (By similarity).By similarity
Asymmetric dimethylation at Arg-18 (H3R17me2a) is linked to gene activation. Asymmetric dimethylation at Arg-3 (H3R2me2a) by prmt6 is linked to gene repression and is mutually exclusive with H3 Lys-5 methylation (H3K4me2 and H3K4me3). H3R2me2a is present at the 3' of genes regardless of their transcription state and is enriched on inactive promoters, while it is absent on active promoters (By similarity).By similarity
Specifically enriched in modifications associated with active chromatin such as methylation at Lys-5 (H3K4me), Lys-37 (H3K36me) and Lys-80 (H3K79me) are linked to gene activation. Methylation at Lys-5 (H3K4me) facilitates subsequent acetylation of H3 and H4. Methylation at Lys-80 (H3K79me) is associated with DNA double-strand break (DSB) responses and is a specific target for tp53bp1. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me) are linked to gene repression. Methylation at Lys-10 (H3K9me) is a specific target for HP1 proteins (cbx1, cbx3 and cbx5) and prevents subsequent phosphorylation at Ser-11 (H3S10ph) and acetylation of H3 and H4. Methylation at Lys-5 (H3K4me) and Lys-80 (H3K79me) require preliminary monoubiquitination of H2B at 'Lys-120' (By similarity).By similarity
Phosphorylated at Thr-4 (H3T3ph) by HASPIN during prophase and dephosphorylated during anaphase. Phosphorylation at Ser-11 (H3S10ph) by aurkb is crucial for chromosome condensation and cell-cycle progression during mitosis and meiosis. In addition phosphorylation at Ser-11 (H3S10ph) by RPS6KA4 and RPS6KA5 is important during interphase because it enables the transcription of genes following external stimulation, like mitogens, stress, growth factors or UV irradiation and result in the activation of genes, such as c-fos and c-jun. Phosphorylation at Ser-11 (H3S10ph), which is linked to gene activation, prevents methylation at Lys-10 (H3K9me) but facilitates acetylation of H3 and H4. Phosphorylation at Ser-11 (H3S10ph) by aurkb mediates the dissociation of HP1 proteins (cbx1, cbx3 and cbx5) from heterochromatin. Phosphorylation at Ser-11 (H3S10ph) is also an essential regulatory mechanism for neoplastic cell transformation. Phosphorylated at Ser-29 (H3S28ph) by map3k20 isoform 1, rps6ka5 or aurkb during mitosis or upon ultraviolet B irradiation. Phosphorylation at Thr-7 (H3T6ph) by prkcb is a specific tag for epigenetic transcriptional activation that prevents demethylation of Lys-5 (H3K4me) by lsd1/kdm1a. At centromeres, specifically phosphorylated at Thr-12 (H3T11ph) from prophase to early anaphase, by dapk3 and pkn1. Phosphorylation at Thr-12 (H3T11ph) by pkn1 is a specific tag for epigenetic transcriptional activation that promotes demethylation of Lys-10 (H3K9me) by kdm4c/jmjd2c. Phosphorylation at Tyr-42 (H3Y41ph) by jak2 promotes exclusion of cbx5 (HP1 alpha) from chromatin. Phosphorylation on Ser-32 (H3S31ph) is specific to regions bordering centromeres in metaphase chromosomes.By similarity
Monoubiquitinated by rag1 in lymphoid cells, monoubiquitination is required for V(D)J recombination.By similarity
Lysine deamination at Lys-5 (H3K4all) to form allysine only takes place on H3K4me3 and results in gene repression.By similarity
Butyrylation of histones marks active promoters and competes with histone acetylation. It is present during late spermatogenesis.By similarity
Succinylation at Lys-80 (H3K79succ) by KAT2A takes place with a maximum frequency around the transcription start sites of genes. It gives a specific tag for epigenetic transcription activation.By similarity

Keywords - PTMi

Acetylation, ADP-ribosylation, Hydroxylation, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiQ6PI20
PRIDEiQ6PI20

Expressioni

Developmental stagei

Expressed during S phase, then expression strongly decreases as cell division slows down during the process of differentiation.

Gene expression databases

BgeeiENSDARG00000020504
ExpressionAtlasiQ6PI20 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. Interacts with zmynd11; when trimethylated at 'Lys-36' (H3.3K36me3).By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei32Interaction with zmynd11By similarity1

GO - Molecular functioni

Protein-protein interaction databases

BioGridi95374, 1 interactor
STRINGi7955.ENSDARP00000125972

Structurei

3D structure databases

ProteinModelPortaliQ6PI20
SMRiQ6PI20
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domaini

Specific interaction of trimethylated form at 'Lys-36' (H3.3K36me3) with zmynd11 is mediated by the encapsulation of Ser-32 residue with a composite pocket formed by the tandem bromo-PWWP domains.By similarity

Sequence similaritiesi

Belongs to the histone H3 family.Curated

Phylogenomic databases

eggNOGiKOG1745 Eukaryota
COG2036 LUCA
GeneTreeiENSGT00760000118967
HOGENOMiHOG000155290
HOVERGENiHBG001172
InParanoidiQ6PI20
KOiK11253
OMAiKRIEPEY
OrthoDBiEOG09370ZG5
PhylomeDBiQ6PI20
TreeFamiTF314241

Family and domain databases

Gene3Di1.10.20.10, 1 hit
InterProiView protein in InterPro
IPR009072 Histone-fold
IPR007125 Histone_H2A/H2B/H3
IPR000164 Histone_H3/CENP-A
PANTHERiPTHR11426 PTHR11426, 1 hit
PfamiView protein in Pfam
PF00125 Histone, 1 hit
PRINTSiPR00622 HISTONEH3
SMARTiView protein in SMART
SM00428 H3, 1 hit
SUPFAMiSSF47113 SSF47113, 1 hit
PROSITEiView protein in PROSITE
PS00322 HISTONE_H3_1, 1 hit
PS00959 HISTONE_H3_2, 1 hit

Sequencei

Sequence statusi: Complete.

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

Q6PI20-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARTKQTARK STGGKAPRKQ LATKAARKSA PSTGGVKKPH RYRPGTVALR
60 70 80 90 100
EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSAAI GALQEASEAY
110 120 130
LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA
Length:136
Mass (Da):15,328
Last modified:January 23, 2007 - v3
Checksum:i5158ED279E6F9E1C
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti50R → G in AAH45982 (Ref. 1) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC045982 mRNA Translation: AAH45982.1
BC049017 mRNA Translation: AAH49017.1
BC057444 mRNA Translation: AAH57444.1
BC071406 mRNA Translation: AAH71406.1
BC092854 mRNA Translation: AAH92854.1
BC152134 mRNA Translation: AAI52135.1
BC154269 mRNA Translation: AAI54270.1
RefSeqiNP_001017599.1, NM_001017599.1
NP_956297.1, NM_200003.1
NP_957395.1, NM_201101.1
NP_998161.1, NM_212996.1
XP_002664801.1, XM_002664755.5
XP_009290278.1, XM_009292003.2
XP_017209248.1, XM_017353759.1
UniGeneiDr.42924
Dr.75577
Dr.75603
Dr.77073
Dr.91654

Genome annotation databases

EnsembliENSDART00000047269; ENSDARP00000047268; ENSDARG00000033009
ENSDART00000098982; ENSDARP00000089753; ENSDARG00000068436
ENSDART00000137017; ENSDARP00000117879; ENSDARG00000045248
ENSDART00000146211; ENSDARP00000120344; ENSDARG00000020504
ENSDART00000151594; ENSDARP00000125972; ENSDARG00000068436
ENSDART00000151600; ENSDARP00000126130; ENSDARG00000068434
ENSDART00000188898; ENSDARP00000157380; ENSDARG00000111005
ENSDART00000192849; ENSDARP00000154528; ENSDARG00000020504
ENSDART00000193606; ENSDARP00000148220; ENSDARG00000033009
GeneIDi100331798
336231
394076
406269
550262
KEGGidre:100331798
dre:336231
dre:394076
dre:406269
dre:550262

Similar proteinsi

Entry informationi

Entry nameiH33_DANRE
AccessioniPrimary (citable) accession number: Q6PI20
Secondary accession number(s): A5PL96, Q7ZV67
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 17, 2006
Last sequence update: January 23, 2007
Last modified: July 18, 2018
This is version 140 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

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