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Protein

Histone H3.1t

Gene

HIST3H3

Organism
Homo sapiens (Human)
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.

GO - Molecular functioni

  • histone binding Source: UniProtKB
  • nucleosomal DNA binding Source: GO_Central

GO - Biological processi

  • double-strand break repair via nonhomologous end joining Source: Reactome
  • negative regulation of protein oligomerization Source: UniProtKB
  • nucleosome assembly Source: UniProtKB
  • protein heterotetramerization Source: UniProtKB
  • telomere capping Source: Reactome
Complete GO annotation...

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000168148-MONOMER.
ReactomeiR-HSA-1221632. Meiotic synapsis.
R-HSA-171306. Packaging Of Telomere Ends.
R-HSA-201722. Formation of the beta-catenin:TCF transactivating complex.
R-HSA-2299718. Condensation of Prophase Chromosomes.
R-HSA-2559586. DNA Damage/Telomere Stress Induced Senescence.
R-HSA-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
R-HSA-5693571. Nonhomologous End-Joining (NHEJ).
R-HSA-5693607. Processing of DNA double-strand break ends.
R-HSA-69473. G2/M DNA damage checkpoint.
R-HSA-912446. Meiotic recombination.
SIGNORiQ16695.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H3.1t
Short name:
H3/t
Short name:
H3t
Alternative name(s):
H3/g
Gene namesi
Name:HIST3H3
Synonyms:H3FT
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:4778. HIST3H3.

Subcellular locationi

GO - Cellular componenti

  • extracellular exosome Source: UniProtKB
  • nuclear nucleosome Source: UniProtKB
  • nucleoplasm Source: Reactome
  • nucleosome Source: UniProtKB
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi8290.
OpenTargetsiENSG00000168148.
PharmGKBiPA29153.

Polymorphism and mutation databases

BioMutaiHIST3H3.
DMDMi18202512.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00002212482 – 136Histone H3.1tAdd BLAST135

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei3Asymmetric dimethylarginine; by PRMT6; alternateBy similarity1
Modified residuei3Citrulline; alternateBy similarity1
Modified residuei4Phosphothreonine; by GSG2By similarity1
Modified residuei5Allysine; alternateBy similarity1
Modified residuei5N6,N6,N6-trimethyllysine; alternateBy similarity1
Modified residuei5N6,N6-dimethyllysine; alternateBy similarity1
Modified residuei5N6-acetyllysine; alternateBy similarity1
Modified residuei5N6-methyllysine; alternateBy similarity1
Modified residuei7Phosphothreonine; by PKCBy similarity1
Modified residuei9Citrulline; alternateBy similarity1
Modified residuei9Symmetric dimethylarginine; by PRMT5; alternateBy similarity1
Modified residuei10N6,N6,N6-trimethyllysine; alternateBy similarity1
Modified residuei10N6,N6-dimethyllysine; alternateBy similarity1
Modified residuei10N6-acetyllysine; alternateBy similarity1
Modified residuei10N6-methyllysine; alternateBy similarity1
Modified residuei11Phosphoserine; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5By similarity1
Modified residuei12Phosphothreonine; by PKCBy similarity1
Modified residuei15N6-acetyllysineBy similarity1
Modified residuei18Asymmetric dimethylarginine; by CARM1; alternateBy similarity1
Modified residuei18Citrulline; alternateBy similarity1
Modified residuei19N6-acetyllysine; alternateCombined sources1
Modified residuei19N6-methyllysine; alternateBy similarity1
Modified residuei24N6-acetyllysine; alternateCombined sources1
Modified residuei24N6-methyllysine; alternateBy similarity1
Modified residuei27CitrullineBy similarity1
Modified residuei28N6,N6,N6-trimethyllysine; alternateBy similarity1
Modified residuei28N6,N6-dimethyllysine; alternateBy similarity1
Modified residuei28N6-acetyllysine; alternateBy similarity1
Modified residuei28N6-methyllysine; alternateBy similarity1
Modified residuei29Phosphoserine; by AURKB, AURKC and RPS6KA5Combined sources1
Modified residuei37N6,N6,N6-trimethyllysine; alternateBy similarity1
Modified residuei37N6,N6-dimethyllysine; alternateBy similarity1
Modified residuei37N6-acetyllysine; alternateBy similarity1
Modified residuei37N6-methyllysine; alternateBy similarity1
Modified residuei38N6-methyllysineBy similarity1
Modified residuei42PhosphotyrosineBy similarity1
Modified residuei57N6,N6,N6-trimethyllysine; alternateBy similarity1
Modified residuei57N6-acetyllysine; alternateBy similarity1
Modified residuei57N6-methyllysine; by EHMT2; alternateBy similarity1
Modified residuei58Phosphoserine1 Publication1
Modified residuei65N6-methyllysineBy similarity1
Modified residuei80N6,N6,N6-trimethyllysine; alternateBy similarity1
Modified residuei80N6,N6-dimethyllysine; alternateBy similarity1
Modified residuei80N6-acetyllysine; alternateBy similarity1
Modified residuei80N6-methyllysine; alternateBy similarity1
Modified residuei81Phosphothreonine1 Publication1
Modified residuei87PhosphoserineBy similarity1
Modified residuei108PhosphothreonineBy similarity1
Modified residuei116N6-acetyllysineBy similarity1
Modified residuei123N6-acetyllysine; alternateBy similarity1
Modified residuei123N6-methyllysine; alternateBy similarity1

Post-translational modificationi

Acetylation is generally linked to gene activation. Acetylation on Lys-10 (H3K9ac) impairs methylation at Arg-9 (H3R8me2s). 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
Citrullination at Arg-9 (H3R8ci) and/or Arg-18 (H3R17ci) by PADI4 impairs methylation and represses transcription.By similarity
Asymmetric dimethylation at Arg-18 (H3R17me2a) by CARM1 is linked to gene activation. Symmetric dimethylation at Arg-9 (H3R8me2s) by PRMT5 is linked to gene repression. 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), 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'. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me) are enriched in inactive X chromosome chromatin. Monomethylation at Lys-57 (H3K56me1) by EHMT2/G9A in G1 phase promotes interaction with PCNA and is required for DNA replication (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. Phosphorylated at Ser-29 (H3S28ph) by MLTK 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 (By similarity).By similarity
Ubiquitinated.By similarity
Lysine deamination at Lys-5 (H3K4all) to form allysine is mediated by LOXL2. Allysine formation by LOXL2 only takes place on H3K4me3 and results in gene repression (By similarity).By similarity

Keywords - PTMi

Acetylation, Citrullination, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ16695.
MaxQBiQ16695.
PaxDbiQ16695.
PeptideAtlasiQ16695.
PRIDEiQ16695.
TopDownProteomicsiQ16695.

PTM databases

iPTMnetiQ16695.
PhosphoSitePlusiQ16695.
SwissPalmiQ16695.

Expressioni

Tissue specificityi

Expressed in testicular cells.

Developmental stagei

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

Gene expression databases

BgeeiENSG00000168148.
CleanExiHS_HIST3H3.
GenevisibleiQ16695. HS.

Organism-specific databases

HPAiCAB001386.
CAB003812.
HPA042570.

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
H2AFXP1610411EBI-358900,EBI-494830
KDM1AO603412EBI-358900,EBI-710124
KDM4AO751646EBI-358900,EBI-936709
SFMBT1Q9UHJ34EBI-358900,EBI-747398

GO - Molecular functioni

  • histone binding Source: UniProtKB

Protein-protein interaction databases

BioGridi113895. 221 interactors.
DIPiDIP-922N.
IntActiQ16695. 24 interactors.
MINTiMINT-1155005.
STRINGi9606.ENSP00000355657.

Structurei

Secondary structure

1136
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 5Combined sources3
Helixi46 – 57Combined sources12
Helixi65 – 76Combined sources12
Turni77 – 79Combined sources3
Beta strandi80 – 82Combined sources3
Helixi87 – 114Combined sources28
Beta strandi118 – 120Combined sources3
Helixi122 – 131Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2V1DX-ray3.10C2-22[»]
2YBPX-ray2.02C/D31-42[»]
2YBSX-ray2.32C/D31-42[»]
3A6NX-ray2.70A/E1-136[»]
3T6RX-ray1.95D2-8[»]
4V2VX-ray2.00C/D26-30[»]
4V2WX-ray1.81C17-36[»]
ProteinModelPortaliQ16695.
SMRiQ16695.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ16695.

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H3 family.Curated

Phylogenomic databases

eggNOGiKOG1745. Eukaryota.
COG2036. LUCA.
GeneTreeiENSGT00760000118967.
HOGENOMiHOG000155290.
HOVERGENiHBG001172.
InParanoidiQ16695.
KOiK11253.
OMAiTIMIQDI.
OrthoDBiEOG091G0XGD.
PhylomeDBiQ16695.
TreeFamiTF314241.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_H2A/H2B/H3.
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.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q16695-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARTKQTARK STGGKAPRKQ LATKVARKSA PATGGVKKPH RYRPGTVALR
60 70 80 90 100
EIRRYQKSTE LLIRKLPFQR LMREIAQDFK TDLRFQSSAV MALQEACESY
110 120 130
LVGLFEDTNL CVIHAKRVTI MPKDIQLARR IRGERA
Length:136
Mass (Da):15,508
Last modified:January 23, 2007 - v3
Checksum:i37375A2C3A377B2B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z49861 Genomic DNA. Translation: CAA90020.1.
AF531308 Genomic DNA. Translation: AAN39284.1.
CR542013 mRNA. Translation: CAG46810.1.
AK312217 mRNA. Translation: BAG35150.1.
AL139288 Genomic DNA. Translation: CAI23333.1.
CH471098 Genomic DNA. Translation: EAW69877.1.
BC069079 mRNA. Translation: AAH69079.1.
BC101837 mRNA. Translation: AAI01838.1.
BC101839 mRNA. Translation: AAI01840.1.
CCDSiCCDS1572.1.
PIRiS57473.
RefSeqiNP_003484.1. NM_003493.2.
UniGeneiHs.248171.

Genome annotation databases

EnsembliENST00000366696; ENSP00000355657; ENSG00000168148.
GeneIDi8290.
KEGGihsa:8290.
UCSCiuc001hsx.1. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z49861 Genomic DNA. Translation: CAA90020.1.
AF531308 Genomic DNA. Translation: AAN39284.1.
CR542013 mRNA. Translation: CAG46810.1.
AK312217 mRNA. Translation: BAG35150.1.
AL139288 Genomic DNA. Translation: CAI23333.1.
CH471098 Genomic DNA. Translation: EAW69877.1.
BC069079 mRNA. Translation: AAH69079.1.
BC101837 mRNA. Translation: AAI01838.1.
BC101839 mRNA. Translation: AAI01840.1.
CCDSiCCDS1572.1.
PIRiS57473.
RefSeqiNP_003484.1. NM_003493.2.
UniGeneiHs.248171.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2V1DX-ray3.10C2-22[»]
2YBPX-ray2.02C/D31-42[»]
2YBSX-ray2.32C/D31-42[»]
3A6NX-ray2.70A/E1-136[»]
3T6RX-ray1.95D2-8[»]
4V2VX-ray2.00C/D26-30[»]
4V2WX-ray1.81C17-36[»]
ProteinModelPortaliQ16695.
SMRiQ16695.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi113895. 221 interactors.
DIPiDIP-922N.
IntActiQ16695. 24 interactors.
MINTiMINT-1155005.
STRINGi9606.ENSP00000355657.

PTM databases

iPTMnetiQ16695.
PhosphoSitePlusiQ16695.
SwissPalmiQ16695.

Polymorphism and mutation databases

BioMutaiHIST3H3.
DMDMi18202512.

Proteomic databases

EPDiQ16695.
MaxQBiQ16695.
PaxDbiQ16695.
PeptideAtlasiQ16695.
PRIDEiQ16695.
TopDownProteomicsiQ16695.

Protocols and materials databases

DNASUi8290.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000366696; ENSP00000355657; ENSG00000168148.
GeneIDi8290.
KEGGihsa:8290.
UCSCiuc001hsx.1. human.

Organism-specific databases

CTDi8290.
DisGeNETi8290.
GeneCardsiHIST3H3.
HGNCiHGNC:4778. HIST3H3.
HPAiCAB001386.
CAB003812.
HPA042570.
MIMi602820. gene.
neXtProtiNX_Q16695.
OpenTargetsiENSG00000168148.
PharmGKBiPA29153.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1745. Eukaryota.
COG2036. LUCA.
GeneTreeiENSGT00760000118967.
HOGENOMiHOG000155290.
HOVERGENiHBG001172.
InParanoidiQ16695.
KOiK11253.
OMAiTIMIQDI.
OrthoDBiEOG091G0XGD.
PhylomeDBiQ16695.
TreeFamiTF314241.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000168148-MONOMER.
ReactomeiR-HSA-1221632. Meiotic synapsis.
R-HSA-171306. Packaging Of Telomere Ends.
R-HSA-201722. Formation of the beta-catenin:TCF transactivating complex.
R-HSA-2299718. Condensation of Prophase Chromosomes.
R-HSA-2559586. DNA Damage/Telomere Stress Induced Senescence.
R-HSA-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
R-HSA-5693571. Nonhomologous End-Joining (NHEJ).
R-HSA-5693607. Processing of DNA double-strand break ends.
R-HSA-69473. G2/M DNA damage checkpoint.
R-HSA-912446. Meiotic recombination.
SIGNORiQ16695.

Miscellaneous databases

EvolutionaryTraceiQ16695.
GeneWikiiHIST3H3.
GenomeRNAii8290.
PROiQ16695.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000168148.
CleanExiHS_HIST3H3.
GenevisibleiQ16695. HS.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_H2A/H2B/H3.
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.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiH31T_HUMAN
AccessioniPrimary (citable) accession number: Q16695
Secondary accession number(s): B2R5K3, Q6FGU4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 26, 2001
Last sequence update: January 23, 2007
Last modified: November 30, 2016
This is version 167 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.