2RSN | pdb_00002rsn

Solution structure of the chromodomain of Chp1 in complex with H3K9me3 peptide

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)
A	SCOP2B Superfamily	Chromo domain-like	8063009	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	e2rsnA1	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
B	peptide from Histone H3	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin oxidoreductase activity, acting on metal ions oxidoreductase activity oxidoreductase activity, acting on metal ions, NAD or NADP as acceptor cupric reductase (NADH) activity catalytic activity	nucleolar large rRNA transcription by RNA polymerase I RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription by RNA polymerase I rRNA transcription nucleolar large rRNA transcription by RNA polymerase I RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription by RNA polymerase I rRNA transcription metabolic process cellular process macromolecule metabolic process rRNA metabolic process regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process inorganic ion homeostasis homeostatic process intracellular copper ion homeostasis copper ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis aerobic respiration cellular respiration energy derivation by oxidation of organic compounds generation of precursor metabolites and energy positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase I positive regulation of cellular process regulation of transcription by RNA polymerase I positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process developmental process sexual sporulation resulting in formation of a cellular spore sexual reproduction reproductive process meiotic cell cycle developmental process involved in reproduction sporulation resulting in formation of a cellular spore anatomical structure morphogenesis sexual sporulation anatomical structure formation involved in morphogenesis anatomical structure development sporulation cell cycle cellular response to stimulus global genome nucleotide-excision repair response to stimulus DNA metabolic process cellular response to stress nucleotide-excision repair DNA damage response response to stress DNA repair cellular component organization chromatin organization cellular component organization or biogenesis	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membraneless organelle transcription regulator complex intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure RNA polymerase I upstream activating factor complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membraneless organelle transcription regulator complex intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure RNA polymerase I upstream activating factor complex RNA polymerase I transcription regulator complex organelle lumen organelle membraneless organelle nuclear lumen CENP-A containing chromatin protein-DNA complex nucleosome chromosome chromatin chromosomal region chromosome, centromeric core domain CENP-A containing nucleosome chromosome, centromeric region
A	Chromo domain-containing protein 1	chromatin binding binding RNA binding nucleic acid binding single-stranded RNA binding DNA binding histone reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity	cellular process cell cycle chromosome segregation cell cycle process regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process cellular process cell cycle chromosome segregation cell cycle process regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process silent mating-type cassette heterochromatin formation negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process pericentric heterochromatin formation siRNA-mediated heterochromatin formation siRNA-mediated pericentric heterochromatin formation regulatory ncRNA-mediated gene silencing regulatory ncRNA-mediated heterochromatin formation subtelomeric heterochromatin formation	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle heterochromatin island chromatin chromosome heterochromatin chromosome, subtelomeric region chromosomal region chromosome, telomeric region subtelomeric heterochromatin intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle heterochromatin island chromatin chromosome heterochromatin chromosome, subtelomeric region chromosomal region chromosome, telomeric region subtelomeric heterochromatin mating-type region heterochromatin cytoplasm pericentric heterochromatin chromosome, centromeric region microtubule organizing center cytoskeleton spindle pole body microtubule cytoskeleton membrane-bounded organelle RITS complex protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membrane-bounded organelle RNAi effector complex intracellular organelle lumen organelle lumen ribonucleoprotein complex nuclear lumen condensed chromosome, centromeric region condensed chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR009072	Histone-fold	Homologous Superfamily
B	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
B	IPR000164	Histone H3/CENP-A	Family
A	IPR048709	Chop1, PIN domain	Domain
A	IPR023780	Chromo domain	Domain
A	IPR049938	Chp1, SPOC domain	Domain
A	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A	IPR023779	Chromo domain, conserved site	Conserved Site
A	IPR051219	Heterochromatin-associated chromo domain-containing protein	Family
A	IPR000953	Chromo/chromo shadow domain	Domain
A	IPR056341	Chp1, domain II	Domain
A	IPR049937	Chp1, chromodomain	Domain
A	IPR035979	RNA-binding domain superfamily	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	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.