3TZD

Crystal structure of the complex of Human Chromobox Homolog 3 (CBX3)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3tzda1	All beta proteins	SH3-like barrel	Chromo domain-like	Chromo domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3tzda2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Chromo domain-like	8062995	3000161	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Chromo	e3tzdA1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: Chromo	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00385	Chromo (CHRromatin Organisation MOdifier) domain (Chromo)	Chromo (CHRromatin Organisation MOdifier) domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Chromobox protein homolog 3	protein binding binding protein domain specific binding chromatin binding transcription factor binding transcription coregulator binding histone methyltransferase binding enzyme binding methylated histone binding modification-dependent protein binding histone binding methylation-dependent protein binding identical protein binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process rhythmic process cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis heterochromatin formation epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic	membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system RNA polymerase II transcription regulator complex protein-containing complex nuclear protein-containing complex transcription regulator complex membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system RNA polymerase II transcription regulator complex protein-containing complex nuclear protein-containing complex transcription regulator complex membraneless organelle chromosome, centromeric region intracellular membraneless organelle chromosome chromosomal region chromatin silencing complex chromatin lock complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen chromatin pericentric heterochromatin heterochromatin organelle inner membrane nuclear membrane membrane nuclear inner membrane organelle membrane cytoskeleton spindle microtubule cytoskeleton condensed chromosome, centromeric region condensed chromosome euchromatin chromosome, telomeric region site of DNA damage
B [auth T]	Histone H1.4	DNA binding double-stranded DNA binding binding organic cyclic compound binding nucleic acid binding chromatin binding chromatin DNA binding histone deacetylase binding protein binding enzyme binding protein-containing complex binding nucleosome binding nucleosomal DNA binding RNA binding DNA binding double-stranded DNA binding binding organic cyclic compound binding nucleic acid binding chromatin binding chromatin DNA binding histone deacetylase binding protein binding enzyme binding protein-containing complex binding nucleosome binding nucleosomal DNA binding RNA binding structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organelle organization protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organelle organization chromosome condensation chromosome organization regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of biological process negative regulation of transcription by RNA polymerase II negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of DNA recombination DNA recombination DNA metabolic process negative regulation of DNA recombination negative regulation of DNA metabolic process regulation of DNA metabolic process	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin euchromatin protein-containing complex protein-DNA complex nucleosome membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin euchromatin protein-containing complex protein-DNA complex nucleosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR023780	Chromo domain	Domain
A	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A	IPR023779	Chromo domain, conserved site	Conserved Site
A	IPR008251	Chromo shadow domain	Domain
A	IPR051219	Heterochromatin-associated chromo domain-containing protein	Family
A	IPR038033	Chromobox protein homologue 3, chromo domain	Domain
A	IPR000953	Chromo/chromo shadow domain	Domain
A	IPR017984	Chromo domain subgroup	Domain
B [auth T]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
B [auth T]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
B [auth T]	IPR005818	Linker histone H1/H5, domain H15	Domain
B [auth T]	IPR005819	Linker histone H1/H5	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q13185	myopathy osteosarcoma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma acute myeloid leukemia primitive neuroectodermal tumor atypical teratoid rhabdoid tumor dermatomyositis gastric carcinoma lung adenocarcinoma malignant ependymoma medulloblastoma nasopharyngeal carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm myopathy osteosarcoma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma acute myeloid leukemia primitive neuroectodermal tumor atypical teratoid rhabdoid tumor dermatomyositis gastric carcinoma lung adenocarcinoma malignant ependymoma medulloblastoma nasopharyngeal carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm plasma cell myeloma adenoma psoriasis breast cancer diabetes mellitus glioblastoma lung cancer malignant glioma metabolic syndrome X oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primary hyperoxaluria type 1 astrocytic tumor rheumatoid arthritis Crohn disease esophageal adenocarcinoma large cell medulloblastoma lymphoplasmacytic lymphoma malignant pancreatic neoplasm
B [auth T]	Pharos: P10412	adenoid cystic carcinoma salivary gland adenoid cystic carcinoma squamous cell lung carcinoma breast cancer endogenous depression gout intellectual disability multiple sclerosis allergic rhinitis colorectal cancer gastric cancer hepatocellular carcinoma lung adenocarcinoma osteoarthritis schizophrenia adenoid cystic carcinoma salivary gland adenoid cystic carcinoma squamous cell lung carcinoma breast cancer endogenous depression gout intellectual disability multiple sclerosis allergic rhinitis colorectal cancer gastric cancer hepatocellular carcinoma lung adenocarcinoma osteoarthritis schizophrenia autism spectrum disorder diabetes mellitus gastric carcinoma hypertensive disorder lung cancer Rahman syndrome

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth T]	MLY	Parent Component: LYS RESID: AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.