3OIJ | pdb_00003oij

Crystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 2 molecules of cognate RNA

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	alpha/beta knot	8037153	3001122	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	alpha/beta knot	8037153	3001122	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	FAD_binding_4	e3oijB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
A	FAD_binding_4	e3oijA1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)
A	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03587	EMG1/NEP1 methyltransferase (EMG1)	EMG1/NEP1 methyltransferase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	5'-R(GPGPGPCPUPUPCPAPAPCPGPCPCPC)-3'	-	-	-
A, B	Essential for mitotic growth 1	RNA binding binding rRNA binding nucleic acid binding RNA methyltransferase activity rRNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity catalytic activity, acting on a rRNA S-adenosylmethionine-dependent methyltransferase activity rRNA (pseudouridine) methyltransferase activity methyltransferase activity RNA binding binding rRNA binding nucleic acid binding RNA methyltransferase activity rRNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity catalytic activity, acting on a rRNA S-adenosylmethionine-dependent methyltransferase activity rRNA (pseudouridine) methyltransferase activity methyltransferase activity catalytic activity identical protein binding protein binding	ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process maturation of SSU-rRNA cellular component organization or biogenesis RNA processing rRNA metabolic process endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process maturation of SSU-rRNA cellular component organization or biogenesis RNA processing rRNA metabolic process endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process ribosomal small subunit biogenesis nucleic acid metabolic process biosynthetic process cellular process metabolic process macromolecule metabolic process endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) rRNA methylation rRNA modification macromolecule methylation RNA modification methylation macromolecule modification rRNA base methylation RNA methylation endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) maturation of 5.8S rRNA maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) rRNA 5'-end processing endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) RNA 5'-end processing	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen protein-containing complex preribosome nuclear protein-containing complex small-subunit processome ribonucleoprotein complex 90S preribosome nuclear periphery cytoplasm polymeric cytoskeletal fiber cytoskeleton nuclear microtubule supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR029026	tRNA (guanine-N1-)-methyltransferase, N-terminal	Homologous Superfamily
A, B	IPR005304	Ribosomal biogenesis, methyltransferase, EMG1/NEP1	Family
A, B	IPR029028	Alpha/beta knot methyltransferases	Homologous Superfamily

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.