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Protein

Histone H3.3C

Gene

h3f3c

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.

GO - Molecular functioni

  1. DNA binding Source: UniProtKB-KW
Complete GO annotation...

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H3.3C
Gene namesi
Name:h3f3c
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Subcellular locationi

GO - Cellular componenti

  1. nucleosome Source: UniProtKB-KW
  2. nucleus Source: UniProtKB-SubCell
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 – 136135Histone H3.3CPRO_0000221266Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei3 – 31Asymmetric dimethylarginine; by PRMT6By similarity
Modified residuei4 – 41Phosphothreonine; by GSG2By similarity
Modified residuei5 – 51Allysine; alternateBy similarity
Modified residuei5 – 51N6,N6,N6-trimethyllysine; alternateBy similarity
Modified residuei5 – 51N6,N6-dimethyllysine; alternateBy similarity
Modified residuei5 – 51N6-acetyllysine; alternateBy similarity
Modified residuei5 – 51N6-methyllysine; alternateBy similarity
Modified residuei7 – 71Phosphothreonine; by PKCBy similarity
Modified residuei10 – 101N6-methylated lysineBy similarity
Modified residuei11 – 111Phosphoserine; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5By similarity
Modified residuei12 – 121Phosphothreonine; by PKCBy similarity
Modified residuei15 – 151N6-acetyllysineBy similarity
Modified residuei18 – 181Asymmetric dimethylarginineBy similarity
Modified residuei19 – 191N6-acetyllysine; alternateBy similarity
Modified residuei19 – 191N6-methylated lysine; alternateBy similarity
Modified residuei24 – 241N6-acetyllysineBy similarity
Modified residuei28 – 281N6-acetyllysine; alternateBy similarity
Modified residuei28 – 281N6-methylated lysine; alternateBy similarity
Modified residuei37 – 371N6-acetyllysine; alternateBy similarity
Modified residuei37 – 371N6-methylated lysine; alternateBy similarity
Modified residuei42 – 421PhosphotyrosineBy similarity
Modified residuei58 – 581PhosphoserineBy similarity
Modified residuei65 – 651N6-methylated lysineBy similarity
Modified residuei80 – 801N6-methylated lysineBy similarity
Modified residuei81 – 811PhosphothreonineBy similarity
Modified residuei116 – 1161N6-acetyllysineBy similarity
Modified residuei123 – 1231N6-acetyllysine; alternateBy similarity
Modified residuei123 – 1231N6-methylated lysine; alternateBy similarity

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
Methylation at Lys-5 (H3K4me) 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 gsg2/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. 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 (By similarity).By similarity
Lysine deamination at Lys-5 (H3K4all) to form allysine only takes place on H3K4me3 and results in gene repression.By similarity

Keywords - PTMi

Acetylation, Methylation, Phosphoprotein

Proteomic databases

PRIDEiP02302.

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.2 Publications

Protein-protein interaction databases

DIPiDIP-39145N.

Structurei

Secondary structure

1
136
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi23 – 253Combined sources
Helixi46 – 5510Combined sources
Helixi65 – 7713Combined sources
Beta strandi80 – 823Combined sources
Helixi87 – 11428Combined sources
Beta strandi118 – 1203Combined sources
Helixi122 – 13211Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AOIX-ray2.80A/E21-136[»]
1M18X-ray2.45A/E2-136[»]
1M19X-ray2.30A/E2-136[»]
1M1AX-ray2.65A/E2-136[»]
ProteinModelPortaliP02302.
SMRiP02302. Positions 2-136.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP02302.

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H3 family.Curated

Phylogenomic databases

HOVERGENiHBG001172.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR000164. Histone_H3/CENP-A.
[Graphical view]
PANTHERiPTHR11426. PTHR11426. 1 hit.
PfamiPF00125. Histone. 1 hit.
[Graphical view]
PRINTSiPR00622. HISTONEH3.
SMARTiSM00428. H3. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00322. HISTONE_H3_1. 1 hit.
PS00959. HISTONE_H3_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P02302-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MARTKQTARK STGGKAPRKQ LVTKAAKKCA PATGGVKKPH RYRPGTVALR
60 70 80 90 100
EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQRSAV MALQEASEAY
110 120 130
LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA
Length:136
Mass (Da):15,487
Last modified:January 23, 2007 - v2
Checksum:iFE1B7E45DBBC7D95
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J00982 Genomic DNA. No translation available.
J00984 Genomic DNA. No translation available.
PIRiA02634. HSXL32.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J00982 Genomic DNA. No translation available.
J00984 Genomic DNA. No translation available.
PIRiA02634. HSXL32.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AOIX-ray2.80A/E21-136[»]
1M18X-ray2.45A/E2-136[»]
1M19X-ray2.30A/E2-136[»]
1M1AX-ray2.65A/E2-136[»]
ProteinModelPortaliP02302.
SMRiP02302. Positions 2-136.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-39145N.

Proteomic databases

PRIDEiP02302.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

HOVERGENiHBG001172.

Miscellaneous databases

EvolutionaryTraceiP02302.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR000164. Histone_H3/CENP-A.
[Graphical view]
PANTHERiPTHR11426. PTHR11426. 1 hit.
PfamiPF00125. Histone. 1 hit.
[Graphical view]
PRINTSiPR00622. HISTONEH3.
SMARTiSM00428. H3. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00322. HISTONE_H3_1. 1 hit.
PS00959. HISTONE_H3_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Primary structure of the histone H3 and H4 genes and their flanking sequences in a minor histone gene cluster of Xenopus laevis."
    Moorman A.F.M., de Boer P.A.J., de Laaf R.T.M., van Dongen W.M.A.M., Destree O.H.J.
    FEBS Lett. 136:45-52(1981) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (GENE CLUSTER X1H1).
  2. "Crystal structure of the nucleosome core particle at 2.8 A resolution."
    Luger K., Mader A.W., Richmond R.K., Sargent D.F., Richmond T.J.
    Nature 389:251-260(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF NUCLEOSOME CORE COMPLEX, SUBUNIT.
  3. "Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands."
    Suto R.K., Edayathumangalam R.S., White C.L., Melander C., Gottesfeld J.M., Dervan P.B., Luger K.
    J. Mol. Biol. 326:371-380(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF NUCLEOSOME CORE COMPLEX, SUBUNIT.

Entry informationi

Entry nameiH3C_XENLA
AccessioniPrimary (citable) accession number: P02302
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: February 4, 2015
This is version 103 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

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.