Annotations: 6K0B

cryo-EM structure of archaeal Ribonuclease P with mature tRNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
L [auth J]	SCOP2B Superfamily	L30e-like	8033665	3001739	SCOP2B (2022-06-29)
E [auth I]	SCOP2B Superfamily	L30e-like	8033665	3001739	SCOP2B (2022-06-29)
J [auth F]	SCOP2B Superfamily	Rof/RNase P subunit-like	8095073	3001815	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	Rof/RNase P subunit-like	8095073	3001815	SCOP2B (2022-06-29)
H [auth B]	SCOP2B Superfamily	Rnp2-like	8095395	3000630	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Rnp2-like	8095395	3000630	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)
L [auth J]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6k0bJ1	A: beta barrels	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (v294.2)
E [auth I]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6k0bI1	A: beta barrels	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (v294.2)
K [auth H]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6k0bH1	A: beta barrels	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (v294.2)
D [auth G]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6k0bG1	A: beta barrels	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (v294.2)
J [auth F]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6k0bF1	A: beta barrels	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (v294.2)
C [auth E]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6k0bE1	A: beta barrels	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (v294.2)
I [auth D]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6k0bD1	A: beta barrels	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (v294.2)
B [auth C]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6k0bC1	A: beta barrels	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (v294.2)
H [auth B]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6k0bB1	A: beta barrels	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (v294.2)
A	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6k0bA1	A: beta barrels	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth I], L [auth J]	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
D [auth G], K [auth H]	PF04032	RNAse P Rpr2/Rpp21/SNM1 subunit domain (Rpr2)	RNAse P Rpr2/Rpp21/SNM1 subunit domain	-	Family
C [auth E], J [auth F]	PF01868	Ribonuclease P/MRP, subunit p29 (RNase_P-MRP_p29)	Ribonuclease P/MRP, subunit p29	This family consists of several archaeal and eukaryotic proteins. The archaeal proteins are found to be expressed within ribosomal operons and several of the sequences are described as ribonuclease P protein subunit p29 proteins [1,2]. The structure ...	This family consists of several archaeal and eukaryotic proteins. The archaeal proteins are found to be expressed within ribosomal operons and several of the sequences are described as ribonuclease P protein subunit p29 proteins [1,2]. The structure of the RNase P subunit, Rpp29, from Methanobacterium thermoautotrophicum has been determined. Mth Rpp29 is a member of the oligonucleotide/oligosaccharide binding fold family. It contains a structured beta-barrel core and unstructured N- and C-terminal extensions bearing several highly conserved amino acid residues that could be involved in RNA contacts in the protein-RNA complex [2]. Rpp29 catalyses the endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. It interacts with the Rpp25 and Pop5 subunits.	Domain
B [auth C], I [auth D]	PF01876	RNase P subunit p30 (RNase_P_p30)	RNase P subunit p30	This protein is part of the RNase P complex that is involved in tRNA maturation [1].	Domain
A, H [auth B]	PF01900	Rpp14/Pop5 family (RNase_P_Rpp14)	Rpp14/Pop5 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G [auth X], N [auth Y]	RPR	-	-	-
F [auth U], M [auth V]	tRNA	-	-	-
E [auth I], L [auth J]	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 box C/D sno(s)RNA binding snoRNA binding 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 protein-containing complex organization small nucleolar ribonucleoprotein complex assembly protein-RNA complex assembly cellular component organization cellular component biogenesis protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis box C/D snoRNP assembly ribosome biogenesis protein metabolic process translation protein biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle ribosome box C/D methylation guide snoRNP complex protein-containing complex sno(s)RNA-containing ribonucleoprotein complex ribonucleoprotein complex box C/D RNP complex
D [auth G], K [auth H]	Ribonuclease P protein component 4	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 cation 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 cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	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	cellular anatomical structure intracellular anatomical structure cytoplasm protein-containing complex endoribonuclease complex catalytic complex ribonuclease P complex ribonucleoprotein complex intracellular protein-containing complex endonuclease complex
C [auth E], J [auth F]	Ribonuclease P protein component 1	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 RNA 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 RNA binding binding nucleic acid binding ribonuclease P RNA binding	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	protein-containing complex endoribonuclease complex catalytic complex sno(s)RNA-containing ribonucleoprotein complex ribonuclease MRP complex ribonucleoprotein complex intracellular protein-containing complex endonuclease complex cellular anatomical structure intracellular anatomical structure cytoplasm ribonuclease P complex
B [auth C], I [auth D]	Ribonuclease P protein component 3	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	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	cellular anatomical structure intracellular anatomical structure cytoplasm protein-containing complex endoribonuclease complex catalytic complex ribonuclease P complex ribonucleoprotein complex intracellular protein-containing complex endonuclease complex
A, H [auth B]	Ribonuclease P protein component 2	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	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	cellular anatomical structure intracellular anatomical structure cytoplasm protein-containing complex endoribonuclease complex catalytic complex ribonuclease P complex ribonucleoprotein complex intracellular protein-containing complex endonuclease complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth I], L [auth J]	IPR050257	Large ribosomal subunit protein eL8/uL1-like	Family
E [auth I], L [auth J]	IPR004038	Ribosomal protein eL8/eL30/eS12/Gadd45	Domain
E [auth I], L [auth J]	IPR022481	Large ribosomal subunit protein eL8, archaea	Family
E [auth I], L [auth J]	IPR004037	Large ribosomal subunit protein eL8-like, conserved site	Conserved Site
E [auth I], L [auth J]	IPR029064	Ribosomal protein eL30-like superfamily	Homologous Superfamily
E [auth I], L [auth J]	IPR018492	Ribosomal protein eL8/Nhp2 family	Family
D [auth G], K [auth H]	IPR007175	Ribonuclease P subunit, Rpr2/Snm1/Rpp21	Family
D [auth G], K [auth H]	IPR016432	Ribonuclease P subunit RNP4	Family
C [auth E], J [auth F]	IPR023538	Ribonuclease P protein subunit RNP1	Family
C [auth E], J [auth F]	IPR036980	Ribonuclease P/MRP subunit Rpp29 superfamily	Homologous Superfamily
C [auth E], J [auth F]	IPR002730	Ribonuclease P protein subunit Rpp29/RNP1	Family
C [auth E], J [auth F]	IPR023534	Rof/RNase P-like	Homologous Superfamily
C [auth E], J [auth F]	IPR016848	Ribonuclease P/MRP subunit Rpp29	Family
B [auth C], I [auth D]	IPR016195	Polymerase/histidinol phosphatase-like	Homologous Superfamily
B [auth C], I [auth D]	IPR023539	Ribonuclease P, protein component 3, archaeal	Family
B [auth C], I [auth D]	IPR002738	RNase P subunit p30	Family
A, H [auth B]	IPR002759	RNase P subunit Pop5/Rpp14/Rnp2-like	Family
A, H [auth B]	IPR038085	RNase P subunit Pop5/Rpp14/Rnp2-like domain superfamily	Homologous Superfamily

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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.