4QUF | pdb_00004quf

crystal structure of chromodomain of Rhino with H3K9me3

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
K [auth F]	SCOP2B Superfamily	Chromo domain-like	8063007	3000161	SCOP2B (2022-06-29)
I [auth E]	SCOP2B Superfamily	Chromo domain-like	8063007	3000161	SCOP2B (2022-06-29)
G [auth D]	SCOP2B Superfamily	Chromo domain-like	8063007	3000161	SCOP2B (2022-06-29)
E [auth C]	SCOP2 Family	Chromo domain	8063006	4000375	SCOP2 (2022-06-29)
E [auth C]	SCOP2 Superfamily	Chromo domain-like	8063007	3000161	SCOP2 (2022-06-29)
C [auth B]	SCOP2B Superfamily	Chromo domain-like	8063007	3000161	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Chromo domain-like	8063007	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)
K [auth F]	Chromo	e4qufF1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: Chromo	ECOD (1.6)
I [auth E]	Chromo	e4qufE1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: Chromo	ECOD (1.6)
G [auth D]	Chromo	e4qufD1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: Chromo	ECOD (1.6)
E [auth C]	Chromo	e4qufC1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: Chromo	ECOD (1.6)
C [auth B]	Chromo	e4qufB1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: Chromo	ECOD (1.6)
A	Chromo	e4qufA1	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)
K [auth F]	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
I [auth E]	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
G [auth D]	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
E [auth C]	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
C [auth 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, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	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
B [auth P], D [auth Q], F [auth R], H [auth T], J [auth V], B [auth P], D [auth Q], F [auth R], H [auth T], J [auth V], L [auth U]	H3(1-15)K9me3 peptide	DNA binding protein-containing complex binding binding chromatin binding nucleic acid binding nucleosome binding nucleosomal DNA binding chromatin DNA binding protein heterodimerization activity protein binding protein dimerization activity 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	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle polytene chromosome chromosome membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle RCAF complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle polytene chromosome chromosome membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle RCAF complex protein-DNA complex nucleosome chromatin
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	RE36324p	chromatin binding binding	negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process cellular component disassembly negative regulation of DNA-templated transcription regulation of biological process negative regulation of cellular component organization negative regulation of metabolic process primary metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of termination of DNA-templated transcription regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cellular component organization transcription antitermination positive regulation of biological process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process cellular component organization nucleic acid biosynthetic process positive regulation of biosynthetic process negative regulation of protein-containing complex disassembly negative regulation of cellular process cellular component organization or biogenesis positive regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process protein-containing complex organization biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process positive regulation of gene expression negative regulation of biosynthetic process cellular process cellular component biogenesis cellular component assembly chromatin organization chromatin remodeling heterochromatin formation epigenetic regulation of gene expression heterochromatin organization negative regulation of gene expression negative regulation of gene expression, epigenetic organelle organization chromosome organization piRNA transcription regulation of piRNA transcription positive regulation of DNA-templated transcription positive regulation of piRNA transcription positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process piRNA processing RNA processing regulatory ncRNA processing regulatory ncRNA-mediated gene silencing positive regulation of snRNA transcription by RNA polymerase II transcription by RNA polymerase II snRNA metabolic process regulation of snRNA transcription by RNA polymerase II snRNA transcription by RNA polymerase II regulation of transcription by RNA polymerase II snRNA transcription positive regulation of transcription by RNA polymerase II multicellular organismal process sexual reproduction cellular developmental process reproductive process cell development cellular process involved in reproduction in multicellular organism pattern specification process developmental process involved in reproduction female gamete generation epithelial cell differentiation gamete generation follicle cell of egg chamber development multicellular organism development cell differentiation anatomical structure development developmental process epithelium development oogenesis multicellular organismal reproductive process tissue development regionalization anatomical structure morphogenesis eggshell formation chorion-containing eggshell formation epithelial cell development chorion-containing eggshell pattern formation anatomical structure formation involved in morphogenesis germ cell development	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle Rhino-Deadlock-Cutoff Complex germ cell nucleus PET complex pericentric heterochromatin chromosomal region chromosome, centromeric region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth P], D [auth Q], F [auth R], H [auth T], J [auth V], B [auth P], D [auth Q], F [auth R], H [auth T], J [auth V], L [auth U]	IPR009072	Histone-fold	Homologous Superfamily
B [auth P], D [auth Q], F [auth R], H [auth T], J [auth V], B [auth P], D [auth Q], F [auth R], H [auth T], J [auth V], L [auth U]	IPR000164	Histone H3/CENP-A	Family
B [auth P], D [auth Q], F [auth R], H [auth T], J [auth V], B [auth P], D [auth Q], F [auth R], H [auth T], J [auth V], L [auth U]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	IPR000953	Chromo/chromo shadow domain	Domain
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	IPR049558	Rhino, chromodomain	Domain
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	IPR023780	Chromo domain	Domain
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	IPR051219	Heterochromatin-associated chromo domain-containing protein	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth P], D [auth Q], F [auth R], H [auth T], J [auth V], B [auth P], D [auth Q], F [auth R], H [auth T], J [auth V], L [auth U]	M3L	Parent Component: LYS RESID: AA0074 PSI-MOD : N6,N6,N6-trimethyl-L-lysine MOD:00083

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.