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Protein

Chromobox protein homolog 3

Gene

CBX3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Seems to be involved in transcriptional silencing in heterochromatin-like complexes. Recognizes and binds histone H3 tails methylated at 'Lys-9', leading to epigenetic repression. May contribute to the association of the heterochromatin with the inner nuclear membrane through its interaction with lamin B receptor (LBR). Involved in the formation of functional kinetochore through interaction with MIS12 complex proteins. Contributes to the conversion of local chromatin to a heterochromatin-like repressive state through H3 'Lys-9' trimethylation, mediates the recruitment of the methyltransferases SUV39H1 and/or SUV39H2 by the PER complex to the E-box elements of the circadian target genes such as PER2 itself or PER1.

GO - Molecular functioni

  • enzyme binding Source: UniProtKB
  • histone methyltransferase binding Source: BHF-UCL
  • protein domain specific binding Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Repressor

Keywords - Biological processi

Biological rhythms, Transcription, Transcription regulation

Enzyme and pathway databases

BioCyciZFISH:ENSG00000122565-MONOMER.
ReactomeiR-HSA-427389. ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression.
R-HSA-73777. RNA Polymerase I Chain Elongation.
SIGNORiQ13185.

Names & Taxonomyi

Protein namesi
Recommended name:
Chromobox protein homolog 3
Alternative name(s):
HECH
Heterochromatin protein 1 homolog gamma
Short name:
HP1 gamma
Modifier 2 protein
Gene namesi
Name:CBX3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 7

Organism-specific databases

HGNCiHGNC:1553. CBX3.

Subcellular locationi

  • Nucleus Curated

  • Note: Associates with euchromatin and is largely excluded from constitutive heterochromatin. May be associated with microtubules and mitotic poles during mitosis (Potential).Curated

GO - Cellular componenti

  • chromatin Source: UniProtKB
  • chromosome, centromeric region Source: CACAO
  • condensed chromosome, centromeric region Source: UniProtKB
  • nuclear chromosome, telomeric region Source: BHF-UCL
  • nuclear envelope Source: UniProtKB
  • nuclear euchromatin Source: UniProtKB
  • nuclear heterochromatin Source: UniProtKB
  • nuclear inner membrane Source: UniProtKB
  • nuclear pericentric heterochromatin Source: UniProtKB
  • nucleus Source: UniProtKB
  • senescence-associated heterochromatin focus Source: Ensembl
  • spindle Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi11335.
OpenTargetsiENSG00000122565.
PharmGKBiPA26128.

Polymorphism and mutation databases

BioMutaiCBX3.
DMDMi116241284.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00000802032 – 183Chromobox protein homolog 3Add BLAST182

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineBy similarity1
Modified residuei5N6-acetyllysine; alternateBy similarity1
Cross-linki5Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Modified residuei10N6-acetyllysine; alternateCombined sources1
Cross-linki10Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Cross-linki21Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei44N6-acetyllysineCombined sources1
Modified residuei50N6-acetyllysineCombined sources1
Modified residuei93PhosphoserineCombined sources1
Modified residuei95PhosphoserineCombined sources1
Modified residuei97PhosphoserineCombined sources1
Modified residuei99PhosphoserineCombined sources1
Cross-linki103Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei176PhosphoserineCombined sources1

Post-translational modificationi

Phosphorylated by PIM1. Phosphorylated during interphase and possibly hyper-phosphorylated during mitosis.2 Publications

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ13185.
MaxQBiQ13185.
PaxDbiQ13185.
PeptideAtlasiQ13185.
PRIDEiQ13185.
TopDownProteomicsiQ13185.

2D gel databases

SWISS-2DPAGEQ13185.

PTM databases

iPTMnetiQ13185.
PhosphoSitePlusiQ13185.
SwissPalmiQ13185.

Expressioni

Gene expression databases

BgeeiENSG00000122565.
CleanExiHS_CBX3.
ExpressionAtlasiQ13185. baseline and differential.
GenevisibleiQ13185. HS.

Organism-specific databases

HPAiCAB001973.
HPA004902.

Interactioni

Subunit structurei

Binds directly to CHAF1A. Interacts with histone H3 methylated at 'Lys-9'. Part of the E2F6.com-1 complex in G0 phase composed of E2F6, MGA, MAX, TFDP1, CBX3, BAT8, EUHMTASE1, RING1, RNF2, MBLR, L3MBTL2 and YAF2. Interacts with LBR, INCENP, TRIM28/TIF1B, KMT5B, KMT5C and SP100. Interacts with TIF1A. Interacts with MIS12 and DSN1. Can interact directly with CBX5 via the chromoshadow domain. Interacts with POGZ. Interacts with CHAMP1. Interacts with ASXL1. The large PER complex involved in the histone methylation is composed of at least PER2, CBX3, TRIM28, SUV39H1 and/or SUV39H2; CBX3 mediates the formation of the complex. Interacts with INCENP.12 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself3EBI-78176,EBI-78176
ADNPQ9H2P03EBI-78176,EBI-1764854
ADNP2Q6IQ322EBI-78176,EBI-2838654
CHAF1AQ131113EBI-78176,EBI-1020839
HIST1H3DP684315EBI-78176,EBI-79722
KMT5CQ86Y972EBI-78176,EBI-7960569
LBRQ147394EBI-78176,EBI-1055147
legAS4Q5ZUS42EBI-78176,EBI-8871796From a different organism.
LRIF1Q5T3J34EBI-78176,EBI-473196
SUV39H1O434636EBI-78176,EBI-349968
TRIM28Q132634EBI-78176,EBI-78139
ZNF280CQ8ND823EBI-78176,EBI-8831272

GO - Molecular functioni

  • enzyme binding Source: UniProtKB
  • histone methyltransferase binding Source: BHF-UCL
  • protein domain specific binding Source: UniProtKB

Protein-protein interaction databases

BioGridi116463. 107 interactors.
DIPiDIP-5985N.
IntActiQ13185. 105 interactors.
MINTiMINT-5002782.
STRINGi9606.ENSP00000336687.

Structurei

Secondary structure

1183
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi29 – 41Combined sources13
Beta strandi44 – 51Combined sources8
Helixi56 – 58Combined sources3
Beta strandi60 – 63Combined sources4
Helixi64 – 66Combined sources3
Helixi70 – 80Combined sources11
Helixi116 – 119Combined sources4
Beta strandi123 – 130Combined sources8
Beta strandi137 – 142Combined sources6
Beta strandi149 – 152Combined sources4
Helixi153 – 159Combined sources7
Helixi161 – 169Combined sources9
Beta strandi172 – 174Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2L11NMR-A29-81[»]
3DM1X-ray2.40A/C/E/G29-86[»]
3KUPX-ray1.77A/B/C/D110-173[»]
3TZDX-ray1.81A29-81[»]
5T1IX-ray1.60A/B110-176[»]
ProteinModelPortaliQ13185.
SMRiQ13185.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ13185.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini30 – 88Chromo 1PROSITE-ProRule annotationAdd BLAST59
Domaini121 – 179Chromo 2; shadow subtypePROSITE-ProRule annotationAdd BLAST59

Sequence similaritiesi

Contains 2 chromo domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG1911. Eukaryota.
ENOG4111JKD. LUCA.
GeneTreeiENSGT00510000046310.
HOGENOMiHOG000220852.
HOVERGENiHBG000400.
InParanoidiQ13185.
KOiK11586.
OMAiRESADKP.
OrthoDBiEOG091G0RBS.
PhylomeDBiQ13185.
TreeFamiTF350503.

Family and domain databases

InterProiIPR000953. Chromo/shadow_dom.
IPR017984. Chromo_dom_subgr.
IPR023780. Chromo_domain.
IPR008251. Chromo_shadow_dom.
IPR016197. Chromodomain-like.
IPR023779. Chromodomain_CS.
[Graphical view]
PfamiPF00385. Chromo. 1 hit.
PF01393. Chromo_shadow. 1 hit.
[Graphical view]
PRINTSiPR00504. CHROMODOMAIN.
SMARTiSM00298. CHROMO. 2 hits.
SM00300. ChSh. 1 hit.
[Graphical view]
SUPFAMiSSF54160. SSF54160. 2 hits.
PROSITEiPS00598. CHROMO_1. 1 hit.
PS50013. CHROMO_2. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q13185-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MASNKTTLQK MGKKQNGKSK KVEEAEPEEF VVEKVLDRRV VNGKVEYFLK
60 70 80 90 100
WKGFTDADNT WEPEENLDCP ELIEAFLNSQ KAGKEKDGTK RKSLSDSESD
110 120 130 140 150
DSKSKKKRDA ADKPRGFARG LDPERIIGAT DSSGELMFLM KWKDSDEADL
160 170 180
VLAKEANMKC PQIVIAFYEE RLTWHSCPED EAQ
Length:183
Mass (Da):20,811
Last modified:October 17, 2006 - v4
Checksum:i5928C63E0C93A76A
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti111A → G in AAH14380 (PubMed:15489334).Curated1
Sequence conflicti111A → V in AAF62370 (Ref. 4) Curated1
Sequence conflicti130T → I in AAB48101 (PubMed:8663349).Curated1
Sequence conflicti130T → I in BAA83340 (PubMed:10664448).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U26312 mRNA. Translation: AAB48101.1.
AB030905 mRNA. Translation: BAA83340.1.
AF136630 mRNA. Translation: AAF62370.1.
BC000954 mRNA. Translation: AAH00954.1.
BC014380 mRNA. Translation: AAH14380.1.
CCDSiCCDS5398.1.
RefSeqiNP_009207.2. NM_007276.4.
NP_057671.2. NM_016587.3.
XP_005249668.1. XM_005249611.3.
UniGeneiHs.381189.

Genome annotation databases

EnsembliENST00000337620; ENSP00000336687; ENSG00000122565.
ENST00000396386; ENSP00000379670; ENSG00000122565.
GeneIDi11335.
KEGGihsa:11335.
UCSCiuc003sxt.4. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U26312 mRNA. Translation: AAB48101.1.
AB030905 mRNA. Translation: BAA83340.1.
AF136630 mRNA. Translation: AAF62370.1.
BC000954 mRNA. Translation: AAH00954.1.
BC014380 mRNA. Translation: AAH14380.1.
CCDSiCCDS5398.1.
RefSeqiNP_009207.2. NM_007276.4.
NP_057671.2. NM_016587.3.
XP_005249668.1. XM_005249611.3.
UniGeneiHs.381189.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2L11NMR-A29-81[»]
3DM1X-ray2.40A/C/E/G29-86[»]
3KUPX-ray1.77A/B/C/D110-173[»]
3TZDX-ray1.81A29-81[»]
5T1IX-ray1.60A/B110-176[»]
ProteinModelPortaliQ13185.
SMRiQ13185.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116463. 107 interactors.
DIPiDIP-5985N.
IntActiQ13185. 105 interactors.
MINTiMINT-5002782.
STRINGi9606.ENSP00000336687.

PTM databases

iPTMnetiQ13185.
PhosphoSitePlusiQ13185.
SwissPalmiQ13185.

Polymorphism and mutation databases

BioMutaiCBX3.
DMDMi116241284.

2D gel databases

SWISS-2DPAGEQ13185.

Proteomic databases

EPDiQ13185.
MaxQBiQ13185.
PaxDbiQ13185.
PeptideAtlasiQ13185.
PRIDEiQ13185.
TopDownProteomicsiQ13185.

Protocols and materials databases

DNASUi11335.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000337620; ENSP00000336687; ENSG00000122565.
ENST00000396386; ENSP00000379670; ENSG00000122565.
GeneIDi11335.
KEGGihsa:11335.
UCSCiuc003sxt.4. human.

Organism-specific databases

CTDi11335.
DisGeNETi11335.
GeneCardsiCBX3.
HGNCiHGNC:1553. CBX3.
HPAiCAB001973.
HPA004902.
MIMi604477. gene.
neXtProtiNX_Q13185.
OpenTargetsiENSG00000122565.
PharmGKBiPA26128.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1911. Eukaryota.
ENOG4111JKD. LUCA.
GeneTreeiENSGT00510000046310.
HOGENOMiHOG000220852.
HOVERGENiHBG000400.
InParanoidiQ13185.
KOiK11586.
OMAiRESADKP.
OrthoDBiEOG091G0RBS.
PhylomeDBiQ13185.
TreeFamiTF350503.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000122565-MONOMER.
ReactomeiR-HSA-427389. ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression.
R-HSA-73777. RNA Polymerase I Chain Elongation.
SIGNORiQ13185.

Miscellaneous databases

ChiTaRSiCBX3. human.
EvolutionaryTraceiQ13185.
GeneWikiiCBX3.
GenomeRNAii11335.
PROiQ13185.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000122565.
CleanExiHS_CBX3.
ExpressionAtlasiQ13185. baseline and differential.
GenevisibleiQ13185. HS.

Family and domain databases

InterProiIPR000953. Chromo/shadow_dom.
IPR017984. Chromo_dom_subgr.
IPR023780. Chromo_domain.
IPR008251. Chromo_shadow_dom.
IPR016197. Chromodomain-like.
IPR023779. Chromodomain_CS.
[Graphical view]
PfamiPF00385. Chromo. 1 hit.
PF01393. Chromo_shadow. 1 hit.
[Graphical view]
PRINTSiPR00504. CHROMODOMAIN.
SMARTiSM00298. CHROMO. 2 hits.
SM00300. ChSh. 1 hit.
[Graphical view]
SUPFAMiSSF54160. SSF54160. 2 hits.
PROSITEiPS00598. CHROMO_1. 1 hit.
PS50013. CHROMO_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCBX3_HUMAN
AccessioniPrimary (citable) accession number: Q13185
Secondary accession number(s): Q96CD7
, Q99409, Q9BVS3, Q9P0Z6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: October 17, 2006
Last modified: November 30, 2016
This is version 180 of the entry and version 4 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, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 7
    Human chromosome 7: 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.