4G56 | pdb_00004g56

Crystal Structure of full length PRMT5/MEP50 complexes from Xenopus laevis

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2 Family	PRMT5 N-terminal domain-like	8046791	4005301	SCOP2 (2022-06-29)
C	SCOP2 Family	Arginine methyltransferase	8046938	4000665	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Xylose isomerase-like	8053411	3000560	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Arginine methyltransferase C-terminal oligomerisation domain-like	8046794	3002184	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8053415	3000118	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Arginine methyltransferase C-terminal oligomerisation domain-like	8046794	3002184	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Xylose isomerase-like	8053411	3000560	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8053415	3000118	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)
D	FAD_binding_3, Amino_oxidase, NAD_binding_8	e4g56D1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: FAD_binding_3, Amino_oxidase, NAD_binding_8	ECOD (develop294)
B	FAD_binding_3, Amino_oxidase, NAD_binding_8	e4g56B1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: FAD_binding_3, Amino_oxidase, NAD_binding_8	ECOD (develop294)
C	Alpha-amylase	e4g56C4	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: Alpha-amylase	ECOD (develop294)
A	JmjC_2	e4g56A1	A: alpha bundles	X: Single-stranded left-handed beta-helix	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: JmjC_2	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat
A, 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	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	PF17286	PRMT5 oligomerisation domain (PRMT5_C)	PRMT5 oligomerisation domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	MGC81050 protein	-	multicellular organismal process sexual reproduction cellular developmental process reproductive process cell development cellular process involved in reproduction in multicellular organism pattern specification process developmental process involved in reproduction female gamete generation gamete generation oocyte development multicellular organism development cell differentiation anatomical structure development multicellular organismal process sexual reproduction cellular developmental process reproductive process cell development cellular process involved in reproduction in multicellular organism pattern specification process developmental process involved in reproduction female gamete generation gamete generation oocyte development multicellular organism development cell differentiation anatomical structure development cell maturation developmental process oocyte axis specification oocyte construction multicellular organismal reproductive process oogenesis developmental maturation anatomical structure maturation germ cell development cellular process oocyte differentiation axis specification	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex methylosome methyltransferase complex transferase complex membrane-bounded organelle histone methyltransferase complex nucleus membrane-enclosed lumen nuclear protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex methylosome methyltransferase complex transferase complex membrane-bounded organelle histone methyltransferase complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
A, C	Hsl7 protein	histone H4 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity protein-arginine N-methyltransferase activity histone methyltransferase activity histone H4R3 methyltransferase activity arginine N-methyltransferase activity protein methyltransferase activity N-methyltransferase activity histone modifying activity methyltransferase activity catalytic activity histone H4 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity protein-arginine N-methyltransferase activity histone methyltransferase activity histone H4R3 methyltransferase activity arginine N-methyltransferase activity protein methyltransferase activity N-methyltransferase activity histone modifying activity methyltransferase activity catalytic activity transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity histone H2AR3 methyltransferase activity histone H2A methyltransferase activity protein-arginine omega-N symmetric methyltransferase activity E-box binding DNA binding sequence-specific DNA binding 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	cellular response to stimulus regulation of cellular process regulation of cell cycle phase transition response to stimulus signaling G2/M transition of mitotic cell cycle negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle cell communication mitotic G2/M transition checkpoint regulation of mitotic cell cycle cellular response to stimulus regulation of cellular process regulation of cell cycle phase transition response to stimulus signaling G2/M transition of mitotic cell cycle negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle cell communication mitotic G2/M transition checkpoint regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction cell cycle DNA replication checkpoint signaling regulation of cell cycle cell cycle process cell cycle G2/M phase transition regulation of biological process mitotic DNA replication checkpoint signaling negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process biological regulation DNA integrity checkpoint signaling regulation of cell cycle G2/M phase transition negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic cell cycle process negative regulation of cell cycle G2/M phase transition cellular process negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process positive regulation of proteasomal protein catabolic process catabolic process positive regulation of protein metabolic process positive regulation of biological process macromolecule catabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of protein metabolic process proteasomal protein catabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of proteasomal protein catabolic process regulation of protein catabolic process cell division mitotic nuclear division regulation of cellular component organization organelle fission regulation of mitotic nuclear division regulation of organelle organization cellular component organization organelle organization nuclear division regulation of nuclear division cellular component organization or biogenesis methylation Golgi ribbon formation Golgi organization endomembrane system organization rhythmic process circadian regulation of gene expression circadian rhythm	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 nucleus

InterPro: Protein Family Classification InterPro Database Homepage

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

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.