9ISZ | pdb_00009isz

Structure of Clr4 catalyzing K14-ubiquitinated histone H3 K9 methylation

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CXC domain-like	8051804	3002037	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SET domain	8043806	3000162	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SET domain	8043806	3000162	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CXC domain-like	8051804	3002037	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain
A, B	PF00856	SET domain (SET)	SET domain	-	Family
A, B	PF05033	Pre-SET motif (Pre-SET)	Pre-SET motif	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F	Histone H3.1/H3.2	DNA binding binding nucleic acid binding chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process heterochromatin boundary formation 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 cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process heterochromatin boundary formation 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 biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process mitotic metaphase chromosome alignment mitotic cell cycle metaphase chromosome alignment localization chromosome localization organelle localization mitotic sister chromatid segregation cell cycle chromosome segregation cell cycle process mitotic nuclear division attachment of spindle microtubules to kinetochore sister chromatid biorientation organelle fission attachment of mitotic spindle microtubules to kinetochore chromosome organization sister chromatid segregation mitotic sister chromatid biorientation organelle organization nuclear division mitotic cell cycle process nuclear chromosome segregation pericentric heterochromatin formation constitutive heterochromatin formation	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin chromosome, subtelomeric region chromosomal region chromosome, telomeric region subtelomeric heterochromatin mating-type region heterochromatin intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin chromosome, subtelomeric region chromosomal region chromosome, telomeric region subtelomeric heterochromatin mating-type region heterochromatin membrane-bounded organelle inclusion body nucleus intracellular membrane-bounded organelle nucleolar peripheral inclusion body nuclear inclusion body protein-containing complex protein-DNA complex nucleosome pericentric heterochromatin chromosome, centromeric region
C, D	Ubiquitin	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding RNA binding nucleic acid binding	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process macromolecule metabolic process protein metabolic process protein ubiquitination macromolecule modification catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process macromolecule metabolic process protein metabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol endosome membrane endosome endomembrane system mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
A, B	Histone-lysine N-methyltransferase, H3 lysine-9 specific	protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups histone H3K9 methyltransferase activity transferase activity histone H3K9 trimethyltransferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity catalytic activity protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups histone H3K9 methyltransferase activity transferase activity histone H3K9 trimethyltransferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity catalytic activity histone H3K9 monomethyltransferase activity ubiquitin-modified protein reader activity ubiquitin-modified histone reader activity histone reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity ubiquitin-like protein reader activity molecular adaptor activity RNA binding binding nucleic acid binding single-stranded RNA binding protein binding ubiquitin binding ubiquitin-like protein binding histone H3K9me2 methyltransferase activity DNA binding double-stranded DNA binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding single-stranded DNA binding	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 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 siRNA-independent facultative heterochromatin formation heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process facultative heterochromatin formation cellular process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process methylation constitutive heterochromatin formation silent mating-type cassette heterochromatin formation 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 co-transcriptional gene silencing by RNA interference machinery	intracellular anatomical structure chromosome, subtelomeric region intracellular membraneless organelle chromatin chromosome heterochromatin chromosomal region intracellular organelle cellular anatomical structure organelle membraneless organelle chromosome, telomeric region subtelomeric heterochromatin mating-type region heterochromatin intracellular anatomical structure chromosome, subtelomeric region intracellular membraneless organelle chromatin chromosome heterochromatin chromosomal region intracellular organelle cellular anatomical structure organelle membraneless organelle chromosome, telomeric region subtelomeric heterochromatin mating-type region heterochromatin membrane-bounded organelle protein-containing complex ubiquitin ligase complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen CLRC complex cullin-RING ubiquitin ligase complex nucleoplasm methyltransferase complex histone methyltransferase complex catalytic complex Cul4-RING E3 ubiquitin ligase complex intracellular membrane-bounded organelle nuclear ubiquitin ligase complex organelle lumen intracellular protein-containing complex nuclear lumen cytoplasm pericentric heterochromatin chromosome, centromeric region microtubule organizing center cytoskeleton spindle pole body microtubule cytoskeleton

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F	IPR009072	Histone-fold	Homologous Superfamily
E, F	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
E, F	IPR000164	Histone H3/CENP-A	Family
C, D	IPR019954	Ubiquitin conserved site	Conserved Site
C, D	IPR000626	Ubiquitin-like domain	Domain
C, D	IPR019956	Ubiquitin domain	Domain
C, D	IPR050158	Ubiquitin and ubiquitin-like	Family
C, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, B	IPR007728	Pre-SET domain	Domain
A, B	IPR046341	SET domain superfamily	Homologous Superfamily
A, B	IPR023780	Chromo domain	Domain
A, B	IPR050973	Histone-lysine N-methyltransferase, H3 Lys-9 specific	Family
A, B	IPR001214	SET domain	Domain
A, B	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A, B	IPR023779	Chromo domain, conserved site	Conserved Site
A, B	IPR011381	Histone-lysine N-methyltransferase SUV39H1/2-like	Family
A, B	IPR003616	Post-SET domain	Domain
A, B	IPR000953	Chromo/chromo shadow domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: P0CG48	acute myeloid leukemia heart disease myocardial infarction pancreatic ductal adenocarcinoma astrocytic tumor lung cancer osteosarcoma renal cell carcinoma glioblastoma malignant pancreatic neoplasm ovarian cancer

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.