3PLA

Crystal structure of a catalytically active substrate-bound box C/D RNP from Sulfolobus solfataricus

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	L30e/L7ae ribosomal proteins	8063947	4001513	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	L30e-like	8063948	3001739	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	L30e-like	8063948	3001739	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	L30e-like	8063948	3001739	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063660	3000118	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063660	3000118	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063660	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)
A	Nop_C	e3plaA3	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: Nop C-terminal domain	F: Nop_C	ECOD (1.6)
A	Nop_N	e3plaA2	A: alpha complex topology	X: Nop N-terminal domain (From Topology)	H: Nop N-terminal domain (From Topology)	T: Nop N-terminal domain	F: Nop_N	ECOD (1.6)
A	PRK14552	e3plaA4	A: mixed a+b and a/b	X: Nop N-terminal domain (From Topology)	H: Nop N-terminal domain (From Topology)	T: Nop N-terminal domain	F: PRK14552	ECOD (1.6)
B	Nop_C	e3plaB3	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: Nop C-terminal domain	F: Nop_C	ECOD (1.6)
B	Nop_N	e3plaB2	A: alpha complex topology	X: Nop N-terminal domain (From Topology)	H: Nop N-terminal domain (From Topology)	T: Nop N-terminal domain	F: Nop_N	ECOD (1.6)
B	PRK14552	e3plaB4	A: mixed a+b and a/b	X: Nop N-terminal domain (From Topology)	H: Nop N-terminal domain (From Topology)	T: Nop N-terminal domain	F: PRK14552	ECOD (1.6)
K	Nop_C	e3plaK3	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: Nop C-terminal domain	F: Nop_C	ECOD (1.6)
K	Nop_N	e3plaK2	A: alpha complex topology	X: Nop N-terminal domain (From Topology)	H: Nop N-terminal domain (From Topology)	T: Nop N-terminal domain	F: Nop_N	ECOD (1.6)
K	PRK14552	e3plaK4	A: mixed a+b and a/b	X: Nop N-terminal domain (From Topology)	H: Nop N-terminal domain (From Topology)	T: Nop N-terminal domain	F: PRK14552	ECOD (1.6)
C	Ribosomal_L7Ae_1	e3plaC1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: L30e-like (From Topology)	T: L30e-like	F: Ribosomal_L7Ae_1	ECOD (1.6)
D	Ribosomal_L7Ae_1	e3plaD1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: L30e-like (From Topology)	T: L30e-like	F: Ribosomal_L7Ae_1	ECOD (1.6)
L	Ribosomal_L7Ae_1	e3plaL1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: L30e-like (From Topology)	T: L30e-like	F: Ribosomal_L7Ae_1	ECOD (1.6)
E	Fibrillarin	e3plaE1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Fibrillarin	ECOD (1.6)
F	Fibrillarin	e3plaF1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Fibrillarin	ECOD (1.6)
M	Fibrillarin	e3plaM1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Fibrillarin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.420.220	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	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)
B	3.30.420.220	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	1.10.287.4070	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
B	1.10.246.90	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
K	3.30.420.220	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
K	1.10.287.4070	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
K	1.10.246.90	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
C	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
D	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
L	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
E	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
E	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
F	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
F	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
M	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
M	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, K	PF21572	Archaeal Nop5/56-rel, N-terminal domain (Nop5_56-rel_N_Arc)	Archaeal Nop5/56-rel, N-terminal domain	This domain is found at the N-terminal end of a group of archaeal proteins, including Uncharacterized NOP5 family protein MJ0694 from Methanocaldococcus jannaschii. This domain interacts with fibrillarin, the other subunit of a complex that is critic ...	This domain is found at the N-terminal end of a group of archaeal proteins, including Uncharacterized NOP5 family protein MJ0694 from Methanocaldococcus jannaschii. This domain interacts with fibrillarin, the other subunit of a complex that is critical to modify and process ribosomal RNAs [1-5]. This domain shows a highly conserved folded structure despite low sequence similarity among homologs. It shows four beta-sheets surrounded by four alpha- helices [6] and is found associated with Pfam:PF01798.	Domain
A, B, K	PF01798	snoRNA binding domain, fibrillarin (Nop)	snoRNA binding domain, fibrillarin	-	Family
C, D, L	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
E, F, M	PF01269	Fibrillarin (Fibrillarin)	Fibrillarin	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, K	Pre mRNA splicing protein	RNA binding binding organic cyclic compound binding snoRNA binding nucleic acid binding	-	preribosome protein-containing complex ribonucleoprotein complex small-subunit processome box C/D methylation guide snoRNP complex sno(s)RNA-containing ribonucleoprotein complex box C/D RNP complex
C, D, L	50S ribosomal protein L7Ae	RNA binding binding organic cyclic compound binding rRNA binding nucleic acid binding tRNA-specific ribonuclease activity endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity, acting on a tRNA nuclease activity RNA binding binding organic cyclic compound binding rRNA binding nucleic acid binding tRNA-specific ribonuclease activity endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity, acting on a tRNA nuclease activity hydrolase activity, acting on ester bonds RNA endonuclease activity ribonuclease P activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters catalytic activity structural molecule activity structural constituent of ribosome	cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing tRNA 5'-end processing cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing tRNA 5'-end processing cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process organic cyclic compound metabolic process biosynthetic process ncRNA metabolic process nucleic acid catabolic process RNA 5'-end processing metabolic process cellular process macromolecule metabolic process tRNA 5'-leader removal cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular component organization or biogenesis organonitrogen compound metabolic process organonitrogen compound biosynthetic process translation protein metabolic process	protein-containing complex ribonucleoprotein complex intracellular anatomical structure cytoplasm cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle ribosome non-membrane-bounded organelle
E, F, M	Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase	catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein-glutamine N-methyltransferase activity transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity N-methyltransferase activity protein methyltransferase activity histone modifying activity methyltransferase activity catalytic activity histone H2A methyltransferase activity histone H2AQ104 methyltransferase activity RNA binding catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein-glutamine N-methyltransferase activity transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity N-methyltransferase activity protein methyltransferase activity histone modifying activity methyltransferase activity catalytic activity histone H2A methyltransferase activity histone H2AQ104 methyltransferase activity RNA binding binding organic cyclic compound binding nucleic acid binding RNA methyltransferase activity rRNA methyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a rRNA	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process tRNA processing ncRNA metabolic process organic substance biosynthetic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process tRNA processing ncRNA metabolic process organic substance biosynthetic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA processing sno(s)RNA metabolic process box C/D sno(s)RNA 3'-end processing RNA 3'-end processing sno(s)RNA processing box C/D sno(s)RNA metabolic process box C/D sno(s)RNA processing sno(s)RNA 3'-end processing ribonucleoprotein complex biogenesis rRNA methylation rRNA processing rRNA modification cellular component biogenesis ribosome biogenesis cellular component organization or biogenesis rRNA metabolic process macromolecule methylation RNA modification methylation macromolecule modification RNA methylation	box C/D methylation guide snoRNP complex protein-containing complex sno(s)RNA-containing ribonucleoprotein complex ribonucleoprotein complex box C/D RNP complex
G, H, N	C/D guide RNA	-	-	-
I, J, O	RNA (5'-R(CPCPAPUPGPAPGPUPGPU)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, K	IPR042239	Nop, C-terminal domain	Homologous Superfamily
A, B, K	IPR036070	Nop domain superfamily	Homologous Superfamily
A, B, K	IPR045056	Nucleolar protein Nop56/Nop58	Family
A, B, K	IPR002687	Nop domain	Domain
A, B, K	IPR048896	Nop5/56-related, N-terminal domain	Domain
A, B, K	IPR012976	NOSIC	Domain
A, B, K	IPR047099	Nop5, N-terminal domain superfamily	Homologous Superfamily
C, D, L	IPR004038	Ribosomal protein eL8/eL30/eS12/Gadd45	Domain
C, D, L	IPR022481	Large ribosomal subunit protein eL8, archaea	Family
C, D, L	IPR004037	Large ribosomal subunit protein eL8-like, conserved site	Conserved Site
C, D, L	IPR029064	Ribosomal protein eL30-like superfamily	Homologous Superfamily
C, D, L	IPR018492	Ribosomal protein eL8/Nhp2 family	Family
E, F, M	IPR000692	rRNA 2'-O-methyltransferase fibrillarin-like	Family
E, F, M	IPR020813	Fibrillarin, conserved site	Conserved Site
E, F, M	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.