3NVI | pdb_00003nvi

Structure of N-terminal truncated Nop56/58 bound with L7Ae and box C/D RNA

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d3nvic_	All alpha proteins	Nop domain	Nop domain	automated matches	automated matches	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
A	d3nvia_	All alpha proteins	Nop domain	Nop domain	automated matches	automated matches	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	L30e-like	8033057	3001739	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	L30e-like	8033057	3001739	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		e3nviD1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: zf-rbx1	F:	ECOD (20:10:01)
B		e3nviB1	A: Immunoglobulin-like beta-sandwich	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: G-gamma	F:	ECOD (20:10:01)
C		e3nviC1	A: TBP-like	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Radical_SAM	F:	ECOD (20:10:01)
A		e3nviA1	A: TBP-like	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Radical_SAM	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
B	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
C	1.10.287.4070	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
C	1.10.246.90	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
A	1.10.287.4070	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
A	1.10.246.90	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF01248	Ribosomal protein L7Ae/L30e/S12e/Gadd45 family (Ribosomal_L7Ae)	Ribosomal protein L7Ae/L30e/S12e/Gadd45 family	This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD11 ...	This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118 [1].	Domain
A, C	PF01798	snoRNA binding domain, fibrillarin (Nop)	snoRNA binding domain, fibrillarin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F	RNA (5'-R(CPUPCPUPGPAPCPCPGPAPAPAPGPGPCPGPUPGPAPUPGPAPGPC)-3')	-	-	-
B, D	50S ribosomal protein L7Ae	RNA binding binding rRNA binding nucleic acid binding tRNA-specific ribonuclease activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity, acting on a tRNA hydrolase activity nuclease activity hydrolase activity, acting on ester bonds RNA binding binding rRNA binding nucleic acid binding tRNA-specific ribonuclease activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity, acting on a tRNA hydrolase activity nuclease activity hydrolase activity, acting on ester bonds RNA endonuclease activity ribonuclease P activity catalytic activity structural molecule activity structural constituent of ribosome	RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing RNA 5'-end processing metabolic process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing RNA 5'-end processing metabolic process cellular process macromolecule metabolic process RNA processing tRNA 5'-leader removal tRNA 5'-end processing ribonucleoprotein complex biogenesis rRNA processing cellular component biogenesis ribosome biogenesis cellular component organization or biogenesis rRNA metabolic process protein metabolic process translation protein biosynthetic process	protein-containing complex ribonucleoprotein complex cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle ribosome
A, C	NOP5/NOP56 related protein	RNA binding binding snoRNA binding nucleic acid binding	-	box C/D methylation guide snoRNP complex protein-containing complex sno(s)RNA-containing ribonucleoprotein complex ribonucleoprotein complex box C/D RNP complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR050257	Large ribosomal subunit protein eL8/uL1-like	Family
B, D	IPR004038	Ribosomal protein eL8/eL30/eS12/Gadd45	Domain
B, D	IPR022481	Large ribosomal subunit protein eL8, archaea	Family
B, D	IPR004037	Large ribosomal subunit protein eL8-like, conserved site	Conserved Site
B, D	IPR029064	Ribosomal protein eL30-like superfamily	Homologous Superfamily
B, D	IPR018492	Ribosomal protein eL8/Nhp2 family	Family
A, C	IPR042239	Nop, C-terminal domain	Homologous Superfamily
A, C	IPR036070	Nop domain superfamily	Homologous Superfamily
A, C	IPR045056	Nucleolar protein Nop56/Nop58	Family
A, C	IPR002687	Nop domain	Domain
A, C	IPR029012	Helix hairpin bin domain superfamily	Homologous Superfamily
A, C	IPR048896	Nop5/56-related, N-terminal domain	Domain
A, C	IPR012976	NOSIC	Domain
A, C	IPR047099	Nop5, N-terminal domain superfamily	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.