Q13185 (CBX3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Chromobox protein homolog 3

Alternative name(s):
HECH
Heterochromatin protein 1 homolog gamma
Short name=HP1 gamma
Modifier 2 protein

Gene names

Name:

CBX3

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	183 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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.
Subunit structure	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, SUV420H1, SUV420H2 and SP100. Interacts with TIF1A By similarity. Interacts with MIS12 and DSN1. Can interact directly with CBX5 via the chromoshadow domain. Interacts with POGZ. Interacts with CHAMP1. Interacts with ASXL1. Ref.7 Ref.8 Ref.9 Ref.11 Ref.12 Ref.13 Ref.14 Ref.21 Ref.22 Ref.23
Subcellular location	Nucleus Potential. Note: Associates with euchromatin and is largely excluded from constitutive heterochromatin. May be associated with microtubules and mitotic poles during mitosis Potential. Ref.10
Post-translational modification	Phosphorylated by PIM1. Phosphorylated during interphase and possibly hyper-phosphorylated during mitosis. Ref.3 Ref.10
Sequence similarities	Contains 2 chromo domains.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Domain	Repeat
Molecular function	Chromatin regulator Repressor
PTM	Acetylation Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	chromatin remodeling Non-traceable author statement Ref.1. Source: UniProtKB negative regulation of transcription, DNA-dependent Inferred from direct assay PubMed 9636147. Source: UniProtKB transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	condensed chromosome, centromeric region Inferred from sequence or structural similarity. Source: UniProtKB nuclear centromeric heterochromatin Inferred from sequence or structural similarity. Source: UniProtKB nuclear euchromatin Inferred from direct assay PubMed 11124534. Source: UniProtKB nuclear inner membrane Non-traceable author statement Ref.1. Source: UniProtKB spindle Inferred from direct assay PubMed 11101528. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		2	EBI-78176,EBI-78176
ADNP	Q9H2P0	2	EBI-78176,EBI-1764854
LBR	Q14739	4	EBI-78176,EBI-1055147
TRIM28	Q13263	3	EBI-78176,EBI-78139

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 183

183

Chromobox protein homolog 3

PRO_0000080203

Regions

Domain

30 – 88

59

Chromo 1

Domain

121 – 179

59

Chromo 2; shadow subtype

Amino acid modifications

Modified residue

10

1

N6-acetyllysine Ref.20

Modified residue

44

1

N6-acetyllysine Ref.20

Modified residue

50

1

N6-acetyllysine Ref.20

Modified residue

93

1

Phosphoserine Ref.16 Ref.24 Ref.26

Modified residue

95

1

Phosphoserine Ref.18 Ref.24 Ref.26

Modified residue

97

1

Phosphoserine Ref.26

Modified residue

99

1

Phosphoserine Ref.26

Modified residue

176

1

Phosphoserine Ref.18

Experimental info

Sequence conflict

111

1

A → G in AAH14380. Ref.5

Sequence conflict

111

1

A → V in AAF62370. Ref.4

Sequence conflict

130

1

T → I in AAB48101. Ref.1

Sequence conflict

130

1

T → I in BAA83340. Ref.3

Secondary structure

1

.

.

.

.

.

.

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.

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183

Helix Strand Turn

Details...

Beta strand

29 – 41

13

Beta strand

44 – 51

8

Helix

56 – 58

3

Beta strand

60 – 63

4

Helix

64 – 66

3

Helix

70 – 80

11

Helix

116 – 119

4

Beta strand

123 – 130

8

Beta strand

137 – 142

6

Beta strand

149 – 152

4

Helix

153 – 159

7

Helix

161 – 171

11

Sequences

	Sequence		Length	Mass (Da)
	Q13185 [UniParc]. Last modified October 17, 2006. Version 4. Checksum: 5928C63E0C93A76A	FASTA	183	20,811
	10 20 30 40 50 60 MASNKTTLQK MGKKQNGKSK KVEEAEPEEF VVEKVLDRRV VNGKVEYFLK WKGFTDADNT 70 80 90 100 110 120 WEPEENLDCP ELIEAFLNSQ KAGKEKDGTK RKSLSDSESD DSKSKKKRDA ADKPRGFARG 130 140 150 160 170 180 LDPERIIGAT DSSGELMFLM KWKDSDEADL VLAKEANMKC PQIVIAFYEE RLTWHSCPED EAQ

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Interaction between an integral protein of the nuclear envelope inner membrane and human chromodomain proteins homologous to Drosophila HP1." Ye Q., Worman H.J. J. Biol. Chem. 271:14653-14656(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 11-183.
[2]	Ye Q., Worman H.J. Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases Cited for: SEQUENCE REVISION.
[3]	"Identification of heterochromatin protein 1 (HP1) as a phosphorylation target by Pim-1 kinase and the effect of phosphorylation on the transcriptional repression function of HP1." Koike N., Maita H., Taira T., Ariga H., Iguchi-Ariga S.M.M. FEBS Lett. 467:17-21(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 11-183, PHOSPHORYLATION BY PIM1.
[4]	Chen J.H., Luo W.Q., Hu S.N., Zhou H.J., Huang X.W., Zhou Y., Yuan J.G., Qiang B.Q. Submitted (MAR-1999) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[5]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Bone marrow and Placenta.
[6]	Lubec G., Afjehi-Sadat L. Submitted (MAR-2007) to UniProtKB Cited for: PROTEIN SEQUENCE OF 160-171, MASS SPECTROMETRY. Tissue: Brain and Cajal-Retzius cell.
[7]	"Domain-specific interactions of human HP1-type chromodomain proteins and inner nuclear membrane protein LBR." Ye Q., Callebaut I., Pezhman A., Courvalin J.-C., Worman H.J. J. Biol. Chem. 272:14983-14989(1997) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH LBR AND CBX5.
[8]	"INCENP centromere and spindle targeting: identification of essential conserved motifs and involvement of heterochromatin protein HP1." Ainsztein A.M., Kandels-Lewis S.E., Mackay A.M., Earnshaw W.C. J. Cell Biol. 143:1763-1774(1998) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH INCENP.
[9]	"Interaction of SP100 with HP1 proteins: a link between the promyelocytic leukemia-associated nuclear bodies and the chromatin compartment." Seeler J.-S., Marchio A., Sitterlin D., Transy C., Dejean A. Proc. Natl. Acad. Sci. U.S.A. 95:7316-7321(1998) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH SP100.
[10]	"Localization and phosphorylation of HP1 proteins during the cell cycle in mammalian cells." Minc E., Allory Y., Worman H.J., Courvalin J.-C., Buendia B. Chromosoma 108:220-234(1999) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION, PHOSPHORYLATION.
[11]	"KAP-1 corepressor protein interacts and colocalizes with heterochromatic and euchromatic HP1 proteins: a potential role for Kruppel-associated box-zinc finger proteins in heterochromatin-mediated gene silencing." Ryan R.F., Schultz D.C., Ayyanathan K., Singh P.B., Friedman J.R., Fredericks W.J., Rauscher F.J. III Mol. Cell. Biol. 19:4366-4378(1999) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH TRIM28.
[12]	"Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins." Lachner M., O'Carroll D., Rea S., Mechtler K., Jenuwein T. Nature 410:116-120(2001) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH HISTONE H3 LYS-9.
[13]	"A complex with chromatin modifiers that occupies E2F- and Myc-responsive genes in G0 cells." Ogawa H., Ishiguro K., Gaubatz S., Livingston D.M., Nakatani Y. Science 296:1132-1136(2002) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN COMPLEX WITH E2F6; TFDP1; MAX; MGA; BAT8; EUHMTASE1; RING1; RNF2; MBLR; L3MBTL2 AND YAF2.
[14]	"A conserved Mis12 centromere complex is linked to heterochromatic HP1 and outer kinetochore protein Zwint-1." Obuse C., Iwasaki O., Kiyomitsu T., Goshima G., Toyoda Y., Yanagida M. Nat. Cell Biol. 6:1135-1141(2004) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH MIS12 AND DSN1.
[15]	"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks." Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M. Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. Tissue: Cervix carcinoma.
[16]	"A probability-based approach for high-throughput protein phosphorylation analysis and site localization." Beausoleil S.A., Villen J., Gerber S.A., Rush J., Gygi S.P. Nat. Biotechnol. 24:1285-1292(2006) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-93, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[17]	"Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle." Daub H., Olsen J.V., Bairlein M., Gnad F., Oppermann F.S., Korner R., Greff Z., Keri G., Stemmann O., Mann M. Mol. Cell 31:438-448(2008) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. Tissue: Cervix carcinoma.
[18]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-95 AND SER-176, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[19]	"Large-scale phosphoproteome analysis of human liver tissue by enrichment and fractionation of phosphopeptides with strong anion exchange chromatography." Han G., Ye M., Zhou H., Jiang X., Feng S., Jiang X., Tian R., Wan D., Zou H., Gu J. Proteomics 8:1346-1361(2008) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. Tissue: Liver.
[20]	"Lysine acetylation targets protein complexes and co-regulates major cellular functions." Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M. Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-10; LYS-44 AND LYS-50, MASS SPECTROMETRY.
[21]	"Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers." Vermeulen M., Eberl H.C., Matarese F., Marks H., Denissov S., Butter F., Lee K.K., Olsen J.V., Hyman A.A., Stunnenberg H.G., Mann M. Cell 142:967-980(2010) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH CHAMP1 AND POGZ.
[22]	"ASXL1 represses retinoic acid receptor-mediated transcription through associating with HP1 and LSD1." Lee S.W., Cho Y.S., Na J.M., Park U.H., Kang M., Kim E.J., Um S.J. J. Biol. Chem. 285:18-29(2010) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH ASXL1.
[23]	"Human POGZ modulates dissociation of HP1alpha from mitotic chromosome arms through Aurora B activation." Nozawa R.S., Nagao K., Masuda H.T., Iwasaki O., Hirota T., Nozaki N., Kimura H., Obuse C. Nat. Cell Biol. 12:719-727(2010) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH POGZ.
[24]	"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis." Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M. Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-93 AND SER-95, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[25]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[26]	"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation." Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B. Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-93; SER-95; SER-97 AND SER-99, MASS SPECTROMETRY.
[27]	"Crystal structure of the complex of chromobox homolog 3 (CBX3) [Homo sapiens] and peptide." Structural genomics consortium (SGC) Submitted (FEB-2009) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 29-86 IN COMPLEX WITH PEPTIDE.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

IPI

IPI00297579.

RefSeq

NP_009207.2. NM_007276.4.
NP_057671.2. NM_016587.3.

UniGene

Hs.381189.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2L11	NMR	-	A	29-81	[»]
3DM1	X-ray	2.40	A/C/E/G	29-86	[»]
3KUP	X-ray	1.77	A/B/C/D	110-173	[»]
3TZD	X-ray	1.81	A	29-81	[»]

ProteinModelPortal

Q13185.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-5985N.

IntAct

Q13185. 45 interactions.

MINT

MINT-5002782.

STRING

9606.ENSP00000336687.

PTM databases

PhosphoSite

Q13185.

Polymorphism databases

DMDM

116241284.

2D gel databases

SWISS-2DPAGE

Q13185.

Proteomic databases

PaxDb

Q13185.

PeptideAtlas

Q13185.

PRIDE

Q13185.

Protocols and materials databases

DNASU

11335.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000337620; ENSP00000336687; ENSG00000122565.
ENST00000396386; ENSP00000379670; ENSG00000122565.

GeneID

11335.

KEGG

hsa:11335.

UCSC

uc003sxt.3. human.

Organism-specific databases

CTD

11335.

GeneCards

GC07P026207.

HGNC

HGNC:1553. CBX3.

HPA

CAB001973.
HPA004902.

MIM

604477. gene.

neXtProt

NX_Q13185.

PharmGKB

PA26128.

GenAtlas

Search...

Phylogenomic databases

eggNOG

NOG264487.

HOGENOM

HOG000220852.

HOVERGEN

HBG000400.

InParanoid

Q13185.

KO

K11586.

OMA

REANTRC.

OrthoDB

EOG4N30QB.

PhylomeDB

Q13185.

Gene expression databases

ArrayExpress

Q13185.

Bgee

Q13185.

CleanEx

HS_CBX3.

Genevestigator

Q13185.

GermOnline

ENSG00000122565. Homo sapiens.

Family and domain databases

InterPro

IPR017984. Chromo_dom_subgr.
IPR023780. Chromo_domain.
IPR000953. Chromo_domain/shadow.
IPR008251. Chromo_shadow_dom.
IPR016197. Chromodomain-like.
IPR023779. Chromodomain_CS.
[Graphical view]

Pfam

PF00385. Chromo. 1 hit.
PF01393. Chromo_shadow. 1 hit.
[Graphical view]

PRINTS

PR00504. CHROMODOMAIN.

SMART

SM00298. CHROMO. 2 hits.
SM00300. ChSh. 1 hit.
[Graphical view]

SUPFAM

SSF54160. Chromodomain-like. 2 hits.

PROSITE

PS00598. CHROMO_1. 1 hit.
PS50013. CHROMO_2. 2 hits.
[Graphical view]

ProtoNet

Search...

Other

ChiTaRS

CBX3. human.

EvolutionaryTrace

Q13185.

GenomeRNAi

11335.

NextBio

43065.

SOURCE

Search...

Entry information

Entry name

CBX3_HUMAN

Accession

Primary (citable) accession number: Q13185
Secondary accession number(s): Q96CD7 , Q99409, Q9BVS3, Q9P0Z6

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	October 17, 2006
Last modified:	May 1, 2013
This is version 141 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.