3KUP | pdb_00003kup

Crystal Structure of the CBX3 Chromo Shadow Domain

External Resource: Annotation

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d3kupd_	All beta proteins	SH3-like barrel	Chromo domain-like	Chromo domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3kupc_	All beta proteins	SH3-like barrel	Chromo domain-like	Chromo domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3kupb_	All beta proteins	SH3-like barrel	Chromo domain-like	Chromo domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3kupa_	All beta proteins	SH3-like barrel	Chromo domain-like	Chromo domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	adh_short	e3kupD1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: adh_short	ECOD (v294.1)
C	adh_short	e3kupC1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: adh_short	ECOD (v294.1)
B	adh_short	e3kupB1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: adh_short	ECOD (v294.1)
A	Bac_rhodopsin	e3kupA1	A: a/b three-layered sandwiches	X: Cystatin-like	H: NTF2-like	T: NTF2-like	F: Bac_rhodopsin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
C	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
B	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
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, B, C, D	PF01393	Chromo shadow domain (Chromo_shadow)	Chromo shadow domain	This domain is distantly related to Pfam:PF00385. This domain is always found in association with a chromo domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Chromobox protein homolog 3	histone H3K9me2/3 reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding protein domain specific binding chromatin binding histone H1K26me2 reader activity histone H1 reader activity transcription factor binding transcription coregulator binding histone H3K9me2/3 reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding protein domain specific binding chromatin binding histone H1K26me2 reader activity histone H1 reader activity transcription factor binding transcription coregulator binding histone H1K26me1 reader activity histone methyltransferase binding enzyme 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 response to ketone response to lipid cellular response to endogenous stimulus response to hormone response to steroid hormone cellular response to ketone cellular response to steroid hormone stimulus cellular response to hormone stimulus response to endogenous stimulus cellular response to dexamethasone stimulus response to glucocorticoid cellular response to glucocorticoid stimulus response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to corticosteroid stimulus response to corticosteroid cellular response to chemical stimulus response to chemical cellular response to lipid response to dexamethasone rhythmic process cellular component organization cellular component biogenesis cellular component assembly chromatin organization chromatin remodeling cellular component organization or biogenesis heterochromatin formation epigenetic regulation of gene expression heterochromatin organization 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 intracellular membraneless organelle chromatin chromosome senescence-associated heterochromatin focus heterochromatin chromosome, centromeric region chromosomal region chromatin silencing complex chromatin lock complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen pericentric 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR023780	Chromo domain	Domain
A, B, C, D	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR023779	Chromo domain, conserved site	Conserved Site
A, B, C, D	IPR008251	Chromo shadow domain	Domain
A, B, C, D	IPR051219	Heterochromatin-associated chromo domain-containing protein	Family
A, B, C, D	IPR038033	Chromobox protein homologue 3, chromo domain	Domain
A, B, C, D	IPR000953	Chromo/chromo shadow domain	Domain
A, B, C, D	IPR017984	Chromo domain subgroup	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	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

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.