9OVY | pdb_00009ovy

Cryo-EM structure of human PRMT5:MEP50 in complex with SAH and compounds 16-19F and HJL-1

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)
F [auth C]	SCOP2B Superfamily	Xylose isomerase-like	8053408	3000560	SCOP2B (2022-06-29)
F [auth C]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8053402	3000118	SCOP2B (2022-06-29)
F [auth C]	SCOP2B Superfamily	Arginine methyltransferase C-terminal oligomerisation domain-like	8046793	3002184	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Arginine methyltransferase C-terminal oligomerisation domain-like	8046793	3002184	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8053402	3000118	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Xylose isomerase-like	8053408	3000560	SCOP2B (2022-06-29)
C [auth G]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8053402	3000118	SCOP2B (2022-06-29)
C [auth G]	SCOP2B Superfamily	Arginine methyltransferase C-terminal oligomerisation domain-like	8046793	3002184	SCOP2B (2022-06-29)
C [auth G]	SCOP2B Superfamily	Xylose isomerase-like	8053408	3000560	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Arginine methyltransferase C-terminal oligomerisation domain-like	8046793	3002184	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Xylose isomerase-like	8053408	3000560	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8053402	3000118	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth G], D [auth E], F [auth C]	PF17285	PRMT5 TIM barrel domain (PRMT5_TIM)	PRMT5 TIM barrel domain	This domain corresponds to the N-terminal TIM barrel domain from PRMT5 proteins..	Domain
A, C [auth G], D [auth E], F [auth C]	PF05185	PRMT5 arginine-N-methyltransferase (PRMT5)	PRMT5 arginine-N-methyltransferase	The human homologue of yeast Skb1 (Shk1 kinase-binding protein 1) is PRMT5, an arginine-N-methyltransferase [3][4]. These proteins appear to be key mitotic regulators. They play a role in Jak signalling in higher eukaryotes.	Domain
A, C [auth G], D [auth E], F [auth C]	PF17286	PRMT5 oligomerisation domain (PRMT5_C)	PRMT5 oligomerisation domain		Domain
B, E [auth F], G [auth D]	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth G], D [auth E], F [auth C]	Protein arginine N-methyltransferase 5	p53 binding protein binding binding catalytic activity, acting on a protein transferase activity, transferring one-carbon groups arginine N-methyltransferase activity protein methyltransferase activity N-methyltransferase activity transferase activity methyltransferase activity catalytic activity S-adenosylmethionine-dependent methyltransferase activity protein-arginine N-methyltransferase activity histone H3 methyltransferase activity p53 binding protein binding binding catalytic activity, acting on a protein transferase activity, transferring one-carbon groups arginine N-methyltransferase activity protein methyltransferase activity N-methyltransferase activity transferase activity methyltransferase activity catalytic activity S-adenosylmethionine-dependent methyltransferase activity protein-arginine N-methyltransferase activity histone H3 methyltransferase activity histone modifying activity histone methyltransferase activity protein-arginine omega-N symmetric methyltransferase activity protein heterodimerization activity protein dimerization activity ribonucleoprotein complex binding protein-containing complex binding histone H4 methyltransferase activity histone H4R3 methyltransferase activity transcription corepressor activity transcription regulator activity transcription coregulator activity E-box binding DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding methyl-CpG binding small molecule binding identical protein binding	ribonucleoprotein complex biogenesis regulation of cellular process positive regulation of biological process RNA metabolic process rRNA processing positive regulation of rRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process positive regulation of metabolic process ribosome biogenesis nucleic acid biosynthetic process regulation of RNA metabolic process ribonucleoprotein complex biogenesis regulation of cellular process positive regulation of biological process RNA metabolic process rRNA processing positive regulation of rRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process positive regulation of metabolic process ribosome biogenesis nucleic acid biosynthetic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process cellular component organization or biogenesis RNA processing rRNA metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process regulation of rRNA processing macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling negative regulation of macromolecule metabolic process epigenetic regulation of gene expression negative regulation of metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic DNA-templated transcription termination DNA-templated transcription developmental process multicellular organismal process gland development animal organ development animal organ regeneration liver development regeneration multicellular organism development hepaticobiliary system development anatomical structure development liver regeneration animal gross anatomical part developmental process system development adenylate cyclase-inhibiting dopamine receptor signaling pathway cellular response to stimulus cellular response to nitrogen compound positive regulation of cell communication response to dopamine positive regulation of signal transduction response to stimulus signaling cellular response to dopamine response to monoamine regulation of signal transduction regulation of dopamine receptor signaling pathway cell communication positive regulation of response to stimulus response to catecholamine cellular response to catecholamine stimulus signal transduction regulation of G protein-coupled receptor signaling pathway regulation of signaling regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway G protein-coupled dopamine receptor signaling pathway response to oxygen-containing compound response to nitrogen compound positive regulation of G protein-coupled receptor signaling pathway cellular response to oxygen-containing compound positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway cellular response to chemical stimulus cellular response to monoamine stimulus regulation of response to stimulus response to chemical adenylate cyclase-modulating G protein-coupled receptor signaling pathway regulation of cell communication G protein-coupled receptor signaling pathway positive regulation of dopamine receptor signaling pathway positive regulation of signaling rhythmic process circadian regulation of gene expression circadian rhythm mRNA processing protein-RNA complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly RNA splicing protein-containing complex organization spliceosomal snRNP assembly mRNA metabolic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile protein methylation peptidyl-arginine methylation peptidyl-arginine N-methylation macromolecule methylation protein alkylation methylation macromolecule modification peptidyl-amino acid modification peptidyl-arginine modification protein metabolic process protein modification process regulation of RNA biosynthetic process regulation of DNA-templated transcription regulation of MAPK cascade intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade mitotic nuclear division regulation of cellular component organization regulation of cell cycle process organelle fission regulation of mitotic nuclear division regulation of organelle organization mitotic cell cycle regulation of mitotic cell cycle organelle organization nuclear division mitotic cell cycle process regulation of nuclear division cell cycle regulation of cell cycle cell cycle process Golgi ribbon formation Golgi organization endomembrane system organization signal transduction by p53 class mediator regulation of signal transduction by p53 class mediator positive regulation of nervous system development cellular developmental process regulation of developmental process cell development regulation of neurogenesis regulation of cell differentiation regulation of gliogenesis positive regulation of gliogenesis regulation of cell development regulation of nervous system development positive regulation of developmental process neurogenesis gliogenesis positive regulation of cell differentiation cell differentiation regulation of multicellular organismal process positive regulation of neurogenesis positive regulation of oligodendrocyte differentiation regulation of multicellular organismal development positive regulation of cell development regulation of glial cell differentiation nervous system development positive regulation of glial cell differentiation central nervous system development oligodendrocyte differentiation glial cell differentiation positive regulation of multicellular organismal process regulation of oligodendrocyte differentiation negative regulation of developmental process negative regulation of cell differentiation regulation of mRNA splicing, via spliceosome positive regulation of macromolecule biosynthetic process positive regulation of mRNA metabolic process positive regulation of mRNA processing positive regulation of mRNA splicing, via spliceosome positive regulation of biosynthetic process regulation of mRNA processing regulation of RNA splicing positive regulation of gene expression regulation of mRNA metabolic process positive regulation of RNA splicing endothelial cell activation cell activation	membrane-bounded organelle protein-containing complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm membrane-bounded organelle protein-containing complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle methyltransferase complex nuclear lumen cytoplasm cytosol membraneless organelle intracellular membraneless organelle chromatin chromosome Golgi apparatus endomembrane system methylosome
B, E [auth F], G [auth D]	Methylosome protein 50	sequence-specific DNA binding DNA binding binding nucleoside phosphate binding nucleotide binding nucleic acid binding heterocyclic compound binding methyl-CpG binding small molecule binding transcription coactivator activity transcription regulator activity transcription coregulator activity ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity sequence-specific DNA binding DNA binding binding nucleoside phosphate binding nucleotide binding nucleic acid binding heterocyclic compound binding methyl-CpG binding small molecule binding transcription coactivator activity transcription regulator activity transcription coregulator activity ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity	catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process protein polyubiquitination protein ubiquitination macromolecule modification catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process protein polyubiquitination 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 ribonucleoprotein complex biogenesis regulation of cellular process positive regulation of biological process RNA metabolic process rRNA processing positive regulation of rRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process positive regulation of metabolic process ribosome biogenesis nucleic acid biosynthetic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process cellular component organization or biogenesis RNA processing rRNA metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process regulation of rRNA processing macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process regulation of mRNA splicing, via spliceosome mRNA processing positive regulation of macromolecule biosynthetic process positive regulation of mRNA metabolic process positive regulation of mRNA processing positive regulation of mRNA splicing, via spliceosome positive regulation of biosynthetic process regulation of mRNA processing RNA splicing regulation of RNA splicing mRNA metabolic process RNA splicing, via transesterification reactions positive regulation of gene expression mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile regulation of mRNA metabolic process positive regulation of RNA splicing protein-RNA complex assembly cellular component organization protein-RNA complex organization cellular component assembly protein-containing complex assembly protein-containing complex organization spliceosomal snRNP assembly	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system protein-containing complex catalytic complex methylosome methyltransferase complex transferase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system protein-containing complex catalytic complex methylosome methyltransferase complex transferase complex cytosol cullin-RING ubiquitin ligase complex ubiquitin ligase complex Cul4-RING E3 ubiquitin ligase complex intracellular protein-containing complex Cul4B-RING E3 ubiquitin ligase complex nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth G], D [auth E], F [auth C]	IPR035247	PRMT5, TIM barrel domain	Domain
A, C [auth G], D [auth E], F [auth C]	IPR025799	Protein arginine N-methyltransferase	Family
A, C [auth G], D [auth E], F [auth C]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, C [auth G], D [auth E], F [auth C]	IPR007857	Protein arginine N-methyltransferase PRMT5	Family
A, C [auth G], D [auth E], F [auth C]	IPR035248	PRMT5, oligomerisation domain	Domain
A, C [auth G], D [auth E], F [auth C]	IPR035075	PRMT5 arginine-N-methyltransferase	Domain
B, E [auth F], G [auth D]	IPR019775	WD40 repeat, conserved site	Conserved Site
B, E [auth F], G [auth D]	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
B, E [auth F], G [auth D]	IPR052139	Methylosome Component WDR77	Family
B, E [auth F], G [auth D]	IPR001680	WD40 repeat	Repeat
B, E [auth F], G [auth D]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C [auth G], D [auth E], F [auth C]	: O14744	hypertensive disorder malignant ependymoma oligodendroglioma plantar fibromatosis psoriasis large cell medulloblastoma medulloblastoma osteosarcoma plasma cell myeloma Sjogren syndrome lung cancer non-small cell lung carcinoma ovarian cancer prostate carcinoma spina bifida
B, E [auth F], G [auth D]	: Q9BQA1	lung cancer ovarian neoplasm Malignant neoplasm of ovary ovarian cancer

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

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.