4IKP

Crystal structure of coactivator-associated arginine methyltransferase 1 with methylenesinefungin

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d4ikpb_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Arginine methyltransferase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4ikpa_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Arginine methyltransferase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4ikpc_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Arginine methyltransferase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4ikpd_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Arginine methyltransferase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

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	8053427	3002184	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8046582	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8046582	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Arginine methyltransferase C-terminal oligomerisation domain-like	8053427	3002184	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8046582	3000118	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Arginine methyltransferase C-terminal oligomerisation domain-like	8053427	3002184	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Arginine methyltransferase C-terminal oligomerisation domain-like	8053427	3002184	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8046582	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)
B	PRMT5_C_1	e4ikpB3	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_1	ECOD (1.6)
B	PrmA	e4ikpB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PrmA	ECOD (1.6)
A	PRMT5_C_1	e4ikpA3	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_1	ECOD (1.6)
A	PrmA	e4ikpA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PrmA	ECOD (1.6)
C	PRMT5_C_1	e4ikpC3	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_1	ECOD (1.6)
C	PrmA	e4ikpC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PrmA	ECOD (1.6)
D	PRMT5_C_1	e4ikpD3	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_1	ECOD (1.6)
D	PrmA	e4ikpD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PrmA	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	3.40.50.150	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)
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)
D	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
D	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, C, D	PF22528	Arginine methyltransferase oligomerization subdomain (PRMT_C)	Arginine methyltransferase oligomerization subdomain	This entry represents a domain found C-terminal in protein arginine methyltransferases. This domain is involved in oligomerisation.	Domain
A, B, C, D	PF06325	Ribosomal protein L11 methyltransferase (PrmA) (PrmA)	Ribosomal protein L11 methyltransferase (PrmA)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Histone-arginine methyltransferase CARM1	protein binding binding modification-dependent protein binding lysine-acetylated histone binding histone binding acetylation-dependent protein 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 protein binding binding modification-dependent protein binding lysine-acetylated histone binding histone binding acetylation-dependent protein 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 DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding histone methyltransferase activity histone arginine N-methyltransferase activity histone modifying activity transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity histone H3R17 methyltransferase activity histone H3 methyltransferase activity histone H3R2 methyltransferase activity transcription factor binding DNA-binding transcription factor binding beta-catenin binding nuclear receptor coactivator activity protein-arginine omega-N asymmetric methyltransferase activity	positive regulation of epithelial cell apoptotic process regulation of biological process positive regulation of programmed cell death regulation of cellular process regulation of epithelial cell apoptotic process regulation of apoptotic process biological regulation positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process epithelial cell apoptotic process cellular process apoptotic process positive regulation of epithelial cell apoptotic process regulation of biological process positive regulation of programmed cell death regulation of cellular process regulation of epithelial cell apoptotic process regulation of apoptotic process biological regulation positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process epithelial cell apoptotic process cellular process apoptotic process programmed cell death positive regulation of cellular process cellular response to stimulus intracellular receptor signaling pathway response to stimulus response to lipid signaling regulation of signal transduction hormone-mediated signaling pathway intracellular signal transduction cell communication cellular response to endogenous stimulus response to hormone regulation of intracellular signal transduction response to steroid hormone regulation of intracellular estrogen receptor signaling pathway regulation of intracellular steroid hormone receptor signaling pathway signal transduction nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus response to organic cyclic compound steroid hormone receptor signaling pathway cellular response to hormone stimulus regulation of signaling response to endogenous stimulus cellular response to organic cyclic compound estrogen receptor signaling pathway cellular response to chemical stimulus regulation of response to stimulus response to chemical cellular response to lipid regulation of cell communication nuclear receptor-mediated signaling pathway DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity primary metabolic process DNA metabolic process nucleic acid metabolic process replication fork reversal nucleobase-containing compound metabolic process DNA replication metabolic process macromolecule metabolic process replication fork processing regulation of neuron projection development multicellular organismal process regulation of cellular component organization regulation of developmental process cellular developmental process cell projection organization negative regulation of biological process cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation dendrite development cell differentiation anatomical structure development negative regulation of cellular process cellular component organization or biogenesis negative regulation of cell projection organization system development developmental process plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization negative regulation of developmental process nervous system development negative regulation of neuron projection development negative regulation of dendrite development generation of neurons regulation of dendrite development neuron development regulation of plasma membrane bounded cell projection organization cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation RNA metabolic process regulation of primary 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 regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process transcription by RNA polymerase I positive regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase I positive regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase I positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process response to organophosphorus response to oxygen-containing compound response to nitrogen compound response to purine-containing compound response to cAMP fat cell differentiation positive regulation of fat cell differentiation regulation of cell differentiation positive regulation of developmental process positive regulation of cell differentiation regulation of fat cell differentiation protein methylation peptidyl-arginine methylation macromolecule methylation protein alkylation methylation macromolecule modification peptidyl-amino acid modification peptidyl-arginine modification protein metabolic process protein modification process chromatin organization chromatin remodeling	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 nuclear replication fork intracellular membraneless organelle nuclear chromosome chromosome membraneless organelle replication fork

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR020989	Histone-arginine methyltransferase CARM1, N-terminal	Domain
A, B, C, D	IPR011993	PH-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR055135	Protein arginine N-methyltransferase domain	Domain
A, B, C, D	IPR025799	Protein arginine N-methyltransferase	Family
A, B, C, D	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q86X55	psoriasis non-small cell lung carcinoma osteosarcoma Pustulosis of Palms and Soles ovarian cancer pustulosis palmaris et plantaris

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.