3I3C | pdb_00003i3c

Crystal Structural of CBX5 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	d3i3cd_	All beta proteins	SH3-like barrel	Chromo domain-like	Chromo domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3i3cc_	All beta proteins	SH3-like barrel	Chromo domain-like	Chromo domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3i3cb_	All beta proteins	SH3-like barrel	Chromo domain-like	Chromo domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3i3ca_	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	YgbB	e3i3cD1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v294.1)
C	YgbB	e3i3cC1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v294.1)
B	YgbB	e3i3cB1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v294.1)
A	Pkinase, Kdo	e3i3cA1	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: SH3	T: SH3	F: Pkinase, Kdo	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 5	histone H3K9me2/3 reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity histone deacetylase binding protein binding binding enzyme binding chromatin binding histone H1K26me2 reader activity histone H1 reader activity ribonucleoprotein complex binding histone H3K9me2/3 reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity histone deacetylase binding protein binding binding enzyme binding chromatin binding histone H1K26me2 reader activity histone H1 reader activity ribonucleoprotein complex binding protein-containing complex binding histone H1K26me1 reader activity transcription factor binding DNA-binding transcription factor 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 cellular component organization organelle organization chromosome condensation chromosome organization cellular component organization or biogenesis localization protein localization to chromatin protein localization to chromosome protein localization to organelle macromolecule localization protein localization to heterochromatin intracellular protein localization chromatin organization heterochromatin organization cellular component biogenesis cellular component assembly chromatin remodeling heterochromatin formation epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen organelle envelope nuclear envelope endomembrane system protein-containing complex histone methyltransferase complex catalytic complex nuclear protein-containing complex transferase complex nucleoplasm methyltransferase complex pericentric heterochromatin chromatin chromosome heterochromatin chromosomal region chromosome, centromeric region kinetochore condensed chromosome, centromeric region supramolecular complex condensed chromosome chromocenter histone deacetylase complex transcription regulator complex transcription repressor complex ribonucleoprotein complex 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	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: P45973	colorectal cancer osteosarcoma primary hyperoxaluria type 1 sarcoidosis acute myeloid leukemia astrocytic tumor cystic fibrosis large cell medulloblastoma malignant ependymoma myocardial infarction ovarian cancer primitive neuroectodermal tumor adrenal cortex carcinoma atrial fibrillation colorectal carcinoma colorectal cancer osteosarcoma primary hyperoxaluria type 1 sarcoidosis acute myeloid leukemia astrocytic tumor cystic fibrosis large cell medulloblastoma malignant ependymoma myocardial infarction ovarian cancer primitive neuroectodermal tumor adrenal cortex carcinoma atrial fibrillation colorectal carcinoma glioblastoma lung adenocarcinoma malignant glioma oligodendroglioma Pick disease rheumatoid arthritis Alzheimer disease atypical teratoid rhabdoid tumor Colorectal Neoplasms heart disease lung carcinoma medulloblastoma

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.