3UA4 | pdb_00003ua4

Crystal Structure of Protein Arginine Methyltransferase PRMT5

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)
B	SCOP2B Superfamily	Arginine methyltransferase C-terminal oligomerisation domain-like	8046792	3002184	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Xylose isomerase-like	8053400	3000560	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8053401	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Arginine methyltransferase C-terminal oligomerisation domain-like	8046792	3002184	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8053401	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Xylose isomerase-like	8053400	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	PRMT5_TIM	e3ua4B1	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: Arginine methyltransferase oligomerization subdomain	T: Arginine methyltransferase oligomerization subdomain	F: PRMT5_TIM	ECOD (v294.1)
B	PRMT5	e3ua4B2	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: Arginine methyltransferase oligomerization subdomain	T: Arginine methyltransferase oligomerization subdomain	F: PRMT5	ECOD (v294.1)
B	PRMT5_C	e3ua4B3	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: Arginine methyltransferase oligomerization subdomain	T: Arginine methyltransferase oligomerization subdomain	F: PRMT5_C	ECOD (v294.1)
A	Transpeptidase	e3ua4A1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Transpeptidase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.20.20.150	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Divalent-metal-dependent TIM barrel enzymes	CATH (4.3.0)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
B	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
A, B	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, B	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
A, B	Protein arginine N-methyltransferase 5	p53 binding protein binding binding 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 p53 binding protein binding binding 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 H2A methyltransferase activity protein-arginine omega-N symmetric methyltransferase activity protein-arginine omega-N monomethyltransferase activity transcription factor binding DNA-binding transcription factor binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process response to stimulus response to chemical response to odorant behavior multicellular organismal process locomotory behavior cellular response to stimulus signaling cell death intracellular signal transduction cell communication apoptotic signaling pathway cellular response to stress DNA damage response response to stress intrinsic apoptotic signaling pathway in response to DNA damage signal transduction apoptotic process intrinsic apoptotic signaling pathway programmed cell death methylation negative regulation of signaling negative regulation of intracellular signal transduction regulation of cellular response to stress regulation of signal transduction DNA damage response, signal transduction by p53 class mediator negative regulation of cell communication regulation of intracellular signal transduction regulation of response to stress regulation of signal transduction by p53 class mediator negative regulation of DNA damage response, signal transduction by p53 class mediator regulation of DNA damage response, signal transduction by p53 class mediator negative regulation of signal transduction by p53 class mediator regulation of signaling negative regulation of response to stimulus signal transduction by p53 class mediator negative regulation of signal transduction regulation of response to stimulus regulation of cell communication signal transduction in response to DNA damage	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex transcription repressor complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR035247	PRMT5, TIM barrel domain	Domain
A, B	IPR025799	Protein arginine N-methyltransferase	Family
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B	IPR007857	Protein arginine N-methyltransferase PRMT5	Family
A, B	IPR035248	PRMT5, oligomerisation domain	Domain
A, B	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.