9E3A | pdb_00009e3a

Cryo-EM structure of PRMT5/WDR77 in complex with 6S complex (pICln PBM local refinement)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD 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)
A [auth J]	SCOP2B Superfamily	Xylose isomerase-like	8053408	3000560	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)
B [auth K]		e9e3aK01	A: ATPD N-terminal domain-like	X: N-terminal domain of the delta subunit of the F1F0-ATP synthase	H: Galactose-binding domain-like	T: Flavodoxin_1	F:	ECOD (20:10:01)
C [auth L]		e9e3aL01	A: ATPD N-terminal domain-like	X: N-terminal domain of the delta subunit of the F1F0-ATP synthase	H: Galactose-binding domain-like	T: Flavodoxin_1	F:	ECOD (20:10:01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth J]	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
B [auth K]	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 [auth J]	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 protein-macromolecule adaptor activity molecular adaptor 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	regulation of cellular 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 cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression negative regulation of metabolic process biological regulation regulation of cellular 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 cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression negative regulation of metabolic process biological regulation 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 cellular process macromolecule metabolic process regulation of metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process DNA-templated transcription termination nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process 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 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 positive regulation of biological process 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 positive regulation of cellular process 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 ribonucleoprotein complex biogenesis mRNA processing protein-RNA complex assembly cellular component biogenesis protein-RNA complex organization cellular component assembly protein-containing complex assembly RNA processing 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 primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic 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 metabolic process positive regulation of macromolecule metabolic process positive regulation of mRNA metabolic process positive regulation of RNA 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 [auth K]	Methylosome protein WDR77	transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor 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 transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor 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	multicellular organismal process regulation of cellular process regulation of developmental process prostate gland development regulation of reproductive process reproductive process negative regulation of biological process gland development developmental process involved in reproduction multicellular organism development regulation of epithelial cell proliferation involved in prostate gland development negative regulation of cellular process anatomical structure development reproductive structure development multicellular organismal process regulation of cellular process regulation of developmental process prostate gland development regulation of reproductive process reproductive process negative regulation of biological process gland development developmental process involved in reproduction multicellular organism development regulation of epithelial cell proliferation involved in prostate gland development negative regulation of cellular process anatomical structure development reproductive structure development regulation of multicellular organismal process epithelial cell proliferation system development developmental process negative regulation of cell population proliferation regulation of biological process cell population proliferation reproductive system development negative regulation of developmental process biological regulation animal organ development epithelial cell proliferation involved in prostate gland development urogenital system development negative regulation of epithelial cell proliferation involved in prostate gland development negative regulation of reproductive process regulation of cell population proliferation cellular process regulation of epithelial cell proliferation negative regulation of multicellular organismal process negative regulation of epithelial cell proliferation ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis RNA processing RNA splicing protein-containing complex organization spliceosomal snRNP assembly primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome metabolic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process positive regulation of cell population proliferation positive regulation of biological process positive regulation of cellular process catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process protein 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 regulation of primary metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process sexual reproduction cellular developmental process cell development cellular process involved in reproduction in multicellular organism pattern specification process female gamete generation gamete generation oocyte development cell differentiation cell maturation oocyte axis specification oocyte construction multicellular organismal reproductive process oogenesis developmental maturation anatomical structure maturation germ cell development oocyte differentiation axis specification secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development epithelial cell differentiation prostate glandular acinus development epithelial cell differentiation involved in prostate gland development epithelium development tissue development glandular epithelial cell differentiation columnar/cuboidal epithelial cell differentiation regulation of mRNA splicing, via spliceosome positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of mRNA metabolic process positive regulation of RNA 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen Golgi apparatus endomembrane system protein-containing complex catalytic complex methylosome methyltransferase complex transferase complex cullin-RING ubiquitin ligase complex ubiquitin ligase complex Cul4-RING E3 ubiquitin ligase complex intracellular protein-containing complex Cul4B-RING E3 ubiquitin ligase complex
C [auth L]	Methylosome subunit pICln	RNA binding binding nucleic acid binding	localization transport monoatomic anion transport monoatomic ion transport chloride transport establishment of localization inorganic anion transport RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process localization transport monoatomic anion transport monoatomic ion transport chloride transport establishment of localization inorganic anion transport RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA splicing, via transesterification reactions mRNA cis splicing, via spliceosome mRNA splicing, via spliceosome metabolic process cellular process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process RNA processing regulation of cellular component size homeostatic process cell volume homeostasis biological regulation cellular component organization cellular homeostasis cellular component organization or biogenesis regulation of biological quality regulation of cell size regulation of anatomical structure size regulation of cellular process regulation of mRNA splicing, via spliceosome positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological process positive regulation of mRNA metabolic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of mRNA processing regulation of macromolecule biosynthetic process regulation of metabolic process positive regulation of mRNA splicing, via spliceosome positive regulation of biological process positive regulation of biosynthetic process positive regulation of cellular process regulation of biosynthetic process regulation of mRNA processing regulation of macromolecule metabolic process regulation of RNA splicing positive regulation of gene expression regulation of mRNA metabolic process positive regulation of RNA splicing ribonucleoprotein complex biogenesis protein-RNA complex assembly cellular component biogenesis protein-RNA complex organization cellular component assembly protein-containing complex assembly protein-containing complex organization spliceosomal snRNP assembly	membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection protein-containing complex pICln-Sm protein complex intracellular anatomical structure Sm-like protein family complex cytoplasm intracellular organelle cytoskeleton membraneless organelle membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection protein-containing complex pICln-Sm protein complex intracellular anatomical structure Sm-like protein family complex cytoplasm intracellular organelle cytoskeleton membraneless organelle intracellular membraneless organelle catalytic complex methylosome methyltransferase complex transferase complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle spliceosomal complex ribonucleoprotein complex cytosol cell periphery plasma membrane membrane sperm principal piece 9+2 motile cilium sperm flagellum motile cilium sperm midpiece sperm head-tail coupling apparatus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth J]	IPR035247	PRMT5, TIM barrel domain	Domain
A [auth J]	IPR025799	Protein arginine N-methyltransferase	Family
A [auth J]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A [auth J]	IPR007857	Protein arginine N-methyltransferase PRMT5	Family
A [auth J]	IPR035248	PRMT5, oligomerisation domain	Domain
A [auth J]	IPR035075	PRMT5 arginine-N-methyltransferase	Domain
B [auth K]	IPR019775	WD40 repeat, conserved site	Conserved Site
B [auth K]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
B [auth K]	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
B [auth K]	IPR052139	Methylosome Component WDR77	Family
B [auth K]	IPR001680	WD40 repeat	Repeat
C [auth L]	IPR039924	Protein ICln/Lot5/Saf5	Family
C [auth L]	IPR011993	PH-like domain superfamily	Homologous Superfamily
C [auth L]	IPR003521	ICln	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth J]	Pharos: 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 [auth K]	Pharos: Q9BQA1	lung cancer ovarian neoplasm Malignant neoplasm of ovary ovarian cancer
C [auth L]	Pharos: P54105	melanoma cutaneous melanoma lymphoplasmacytic lymphoma ovarian cancer plasma cell myeloma dermatomyositis pancreatic intraductal papillary-mucinous carcinoma lung cancer osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia

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.