1O9S

Crystal structure of a ternary complex of the human histone methyltransferase SET7/9

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1o9sa1	All beta proteins	open-sided beta-meander	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1o9sa2	All beta proteins	beta-clip	SET domain	Histone lysine methyltransferases	Histone H3 K4-specific methyltransferase SET7/9 catalytic domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1o9sb1	All beta proteins	open-sided beta-meander	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1o9sb2	All beta proteins	beta-clip	SET domain	Histone lysine methyltransferases	Histone H3 K4-specific methyltransferase SET7/9 catalytic domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	SET domain	8042399	3000162	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SET domain	8042399	3000162	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	SET	e1o9sA1	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: SET	ECOD (1.6)
A	KOG1079_3rd_1	e1o9sA2	A: beta meanders	X: open-sided beta-meander	H: Histone H3 K4-specific methyltransferase SET7/9-N (From Topology)	T: Histone H3 K4-specific methyltransferase SET7/9-N	F: KOG1079_3rd_1	ECOD (1.6)
B	SET	e1o9sB1	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: SET	ECOD (1.6)
B	KOG1079_3rd_1	e1o9sB2	A: beta meanders	X: open-sided beta-meander	H: Histone H3 K4-specific methyltransferase SET7/9-N (From Topology)	T: Histone H3 K4-specific methyltransferase SET7/9-N	F: KOG1079_3rd_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.20.110.10	Mainly Beta	Single Sheet	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	CATH (4.3.0)
A	2.170.270.10	Mainly Beta	Beta Complex	Beta-clip-like	SET domain	CATH (4.3.0)
B	2.20.110.10	Mainly Beta	Single Sheet	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	CATH (4.3.0)
B	2.170.270.10	Mainly Beta	Beta Complex	Beta-clip-like	SET domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00856	SET domain (SET)	SET domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-4 SPECIFIC	p53 binding protein binding binding protein-lysine N-methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups lysine N-methyltransferase activity protein methyltransferase activity N-methyltransferase activity transferase activity methyltransferase activity catalytic activity S-adenosylmethionine-dependent methyltransferase activity histone modifying activity p53 binding protein binding binding protein-lysine N-methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups lysine N-methyltransferase activity protein methyltransferase activity N-methyltransferase activity transferase activity methyltransferase activity catalytic activity S-adenosylmethionine-dependent methyltransferase activity histone modifying activity histone methyltransferase activity histone H3 methyltransferase activity histone H3K4 monomethyltransferase activity histone H3K4 methyltransferase activity chromatin binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process peptidyl-lysine methylation protein methylation peptidyl-lysine modification peptidyl-lysine monomethylation primary metabolic process macromolecule methylation protein alkylation methylation cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process peptidyl-lysine methylation protein methylation peptidyl-lysine modification peptidyl-lysine monomethylation primary metabolic process macromolecule methylation protein alkylation methylation macromolecule modification peptidyl-amino acid modification metabolic process protein metabolic process macromolecule metabolic process protein modification process cellular component organization chromatin organization heterochromatin organization cellular component organization or biogenesis peptidyl-lysine dimethylation regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process positive regulation of nucleobase-containing compound metabolic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process response to alcohol response to chemical response to oxygen-containing compound response to ethanol	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 chromosome nucleoplasm
C [auth K], D [auth L]	GENE FRAGMENT FOR HISTONE H3	DNA binding binding organic cyclic compound binding nucleic acid binding cell adhesion molecule binding cadherin binding protein binding protein heterodimerization activity 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 biosynthetic process 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 biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process organelle organization telomere organization chromosome organization regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process	cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle membraneless organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR046341	SET domain superfamily	Homologous Superfamily
A, B	IPR017155	Histone-lysine N-methyltransferase SETD7	Family
A, B	IPR001214	SET domain	Domain
A, B	IPR003409	MORN repeat	Repeat
A, B	IPR044436	SETD7, SET domain	Domain
C [auth K], D [auth L]	IPR009072	Histone-fold	Homologous Superfamily
C [auth K], D [auth L]	IPR007125	Histone H2A/H2B/H3	Domain
C [auth K], D [auth L]	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q8WTS6	atypical teratoid rhabdoid tumor malignant ependymoma pituitary cancer Crohn disease ovarian cancer ulcerative colitis invasive ductal breast carcinoma pancreatic ductal adenocarcinoma
C [auth K], D [auth L]	Pharos: P68431	lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial hypertensive disorder lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis astrocytoma (excluding glioblastoma) pancreatic intraductal papillary-mucinous carcinoma breast cancer spina bifida cystic fibrosis exocrine pancreatic carcinoma glioma susceptibility 1 invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous neoplasm breast carcinoma subependymoma ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C [auth K], D [auth L]	MLZ	Parent Component: LYS RESID: AA0076 PSI-MOD : N6-methyl-L-lysine MOD:00085

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.