4GQB

Crystal Structure of the human PRMT5:MEP50 Complex

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
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	PRMT5 N-terminal domain-like	8046790	4005301	SCOP2 (2022-06-29)
A	SCOP2 Family	Arginine methyltransferase	8046935	4000665	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Xylose isomerase-like	8053408	3000560	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8053402	3000118	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Arginine methyltransferase C-terminal oligomerisation domain-like	8046793	3002184	SCOP2 (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	PRMT5_C	e4gqbA3	A: beta sandwiches	X: Arginine methyltransferase oligomerization subdomain (From Topology)	H: Arginine methyltransferase oligomerization subdomain (From Topology)	T: Arginine methyltransferase oligomerization subdomain	F: PRMT5_C	ECOD (1.6)
A	PRMT5_TIM	e4gqbA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PRMT5_TIM	ECOD (1.6)
A	PRMT5	e4gqbA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PRMT5	ECOD (1.6)
B	ANAPC4_WD40_5	e4gqbB1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: ANAPC4_WD40_5	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.150	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Divalent-metal-dependent TIM barrel enzymes	CATH (4.3.0)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
A	2.70.160.11	Mainly Beta	Distorted Sandwich	Hnrnp arginine n-methyltransferase1	Hnrnp arginine n-methyltransferase1	CATH (4.3.0)
B	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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	PF17286	PRMT5 oligomerisation domain (PRMT5_C)	PRMT5 oligomerisation domain	-	Domain
B	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	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 histone arginine N-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 organic cyclic compound 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 cellular biosynthetic process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation negative regulation of cellular metabolic process 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 regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation negative regulation of cellular metabolic process 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 cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular 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 response to organic cyclic compound positive regulation of cellular process regulation of signaling regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway G protein-coupled dopamine receptor signaling pathway cellular response to organic cyclic compound 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 cell differentiation regulation of neurogenesis 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 regulation of glial cell differentiation positive regulation of cell development 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 nucleobase-containing compound 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 cellular metabolic process 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 positive regulation of cellular biosynthetic process 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 cellular anatomical entity transferase complex intracellular organelle lumen intracellular organelle 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 cellular anatomical entity transferase complex intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle methyltransferase complex nuclear lumen cytoplasm cytosol intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle Golgi apparatus endomembrane system methylosome
B	Methylosome protein 50	ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity sequence-specific DNA binding DNA binding binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding nucleic acid binding heterocyclic compound binding methyl-CpG binding small molecule binding ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity sequence-specific DNA binding DNA binding binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding nucleic acid binding heterocyclic compound binding methyl-CpG binding small molecule binding transcription coactivator activity transcription regulator activity transcription coregulator activity nuclear receptor coactivator activity	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 regulation of biological process negative regulation of cell population proliferation 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 cellular biosynthetic process 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 cellular metabolic process 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 proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis 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 cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic 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 nucleobase-containing compound 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 cellular metabolic process 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 positive regulation of cellular biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen intracellular anatomical structure cytoplasm cellular anatomical entity 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	Histone H4 peptide	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity RNA binding 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 organelle organization 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 organelle organization telomere organization chromosome organization protein localization protein localization to chromatin cellular localization protein localization to chromosome, centromeric region localization protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to CENP-A containing chromatin multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process regulation of megakaryocyte differentiation negative regulation of biological process megakaryocyte differentiation cell development regulation of cell differentiation regulation of cell development multicellular organism development negative regulation of megakaryocyte differentiation cell differentiation anatomical structure development negative regulation of cellular process negative regulation of cell differentiation regulation of immune system process regulation of multicellular organismal process developmental process regulation of biological process regulation of multicellular organismal development hemopoiesis negative regulation of developmental process regulation of myeloid cell differentiation biological regulation negative regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis	membrane cellular anatomical entity 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 CENP-A containing chromatin membrane cellular anatomical entity 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 CENP-A containing chromatin protein-DNA complex nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome intracellular non-membrane-bounded organelle chromosome, centromeric region non-membrane-bounded organelle chromosome, telomeric region 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	IPR035247	PRMT5, TIM barrel domain	Domain
A	IPR025799	Protein arginine N-methyltransferase	Family
A	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A	IPR007857	Protein arginine N-methyltransferase PRMT5	Family
A	IPR035248	PRMT5, oligomerisation domain	Domain
A	IPR035075	PRMT5 arginine-N-methyltransferase	Domain
B	IPR019775	WD40 repeat, conserved site	Conserved Site
B	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
B	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
B	IPR052139	Methylosome Component WDR77	Family
B	IPR001680	WD40 repeat	Repeat
C	IPR009072	Histone-fold	Homologous Superfamily
C	IPR035425	CENP-T/Histone H4, histone fold	Domain
C	IPR001951	Histone H4	Family
C	IPR019809	Histone H4, conserved site	Conserved Site
C	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	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	Pharos: Q9BQA1	lung cancer ovarian neoplasm Malignant neoplasm of ovary ovarian cancer
C	Pharos: P62805	lung carcinoma Malignant neoplasm of breast non-small cell lung carcinoma Pick disease acute myeloid leukemia squamous cell lung carcinoma atypical teratoid rhabdoid tumor breast carcinoma ductal breast carcinoma in situ exocrine pancreatic carcinoma hepatocellular carcinoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis lung carcinoma Malignant neoplasm of breast non-small cell lung carcinoma Pick disease acute myeloid leukemia squamous cell lung carcinoma atypical teratoid rhabdoid tumor breast carcinoma ductal breast carcinoma in situ exocrine pancreatic carcinoma hepatocellular carcinoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis pilocytic astrocytoma allergic rhinitis ulcerative colitis autism spectrum disorder cystic fibrosis endogenous depression glioblastoma hypertensive disorder lung cancer malignant mesothelioma multiple sclerosis osteosarcoma psoriasis astrocytic tumor breast cancer diabetes mellitus endometriosis gout invasive ductal breast carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359

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.