2HVY | pdb_00002hvy

Crystal structure of an H/ACA box RNP from Pyrococcus furiosus

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)
E [auth D]	d2hvyd1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	L30e-like	L30e/L7ae ribosomal proteins	Ribosomal protein L7ae	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
D [auth C]	d2hvyc1	Small proteins	Rubredoxin-like	Nop10-like SnoRNP	Nucleolar RNA-binding protein Nop10-like	Ribosome biogenesis protein Nop10	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
C [auth B]	d2hvyb1	All beta proteins	Reductase/isomerase/elongation factor common domain	Translation proteins	Gar1-like SnoRNP	Gar1 homolog PF1791	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
B [auth A]	d2hvya1	All beta proteins	PUA domain-like	PUA domain-like	PUA domain	Pseudouridine synthase II TruB, C-terminal domain	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
B [auth A]	d2hvya2	Alpha and beta proteins (a+b)	Pseudouridine synthase	Pseudouridine synthase	Pseudouridine synthase II TruB	Pseudouridine synthase II TruB	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth D]	SCOP2 Family	L30e/L7ae ribosomal proteins	8020677	4001513	SCOP2 (2022-06-29)
E [auth D]	SCOP2 Superfamily	L30e-like	8033057	3001739	SCOP2 (2022-06-29)
D [auth C]	SCOP2B Superfamily	Nop10-like SnoRNP Znf-like	8040332	3000486	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Translational proteins	8040331	3000811	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Pseudouridine synthase	8040330	3001360	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	PUA domain-like	8040329	3001015	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)
E [auth D]	Ribosomal_L7Ae_1	e2hvyD1	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 [auth C]	Nop10p	e2hvyC1	A: few secondary structure elements	X: Rubredoxin-like	H: Nucleolar RNA-binding protein Nop10-like (From Topology)	T: Nucleolar RNA-binding protein Nop10-like	F: Nop10p	ECOD (1.6)
C [auth B]	Gar1	e2hvyB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Gar1	ECOD (1.6)
B [auth A]	PUA	e2hvyA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: PUA	ECOD (1.6)
B [auth A]	TruB_N	e2hvyA2	A: a+b two layers	X: Alpha-beta plaits	H: Pseudouridine synthase (From Topology)	T: Pseudouridine synthase	F: TruB_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth D]	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
D [auth C]	2.20.28.40	Mainly Beta	Single Sheet	Rubrerythrin, domain 2	H/ACA ribonucleoprotein complex, subunit Nop10	CATH (4.3.0)
C [auth B]	2.40.10.230	Mainly Beta	Beta Barrel	Thrombin, subunit H	Probable tRNA pseudouridine synthase domain	CATH (4.3.0)
B [auth A]	2.30.130.10	Mainly Beta	Roll	Archaeosine Trna-guanine Transglycosylase	Chain: A, domain 4	CATH (4.3.0)
B [auth A]	3.30.2350.10	Alpha Beta	2-Layer Sandwich	Pseudouridine synthase	Pseudouridine synthase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth 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
C [auth B]	PF04410	Gar1/Naf1 RNA binding region (Gar1)	Gar1/Naf1 RNA binding region	Gar1 is a small nucleolar RNP that is required for pre-mRNA processing and pseudouridylation [1]. It is co-immunoprecipitated with the H/ACA families of snoRNAs. This family represents the conserved central region of Gar1. This region is necessary an ...	Gar1 is a small nucleolar RNP that is required for pre-mRNA processing and pseudouridylation [1]. It is co-immunoprecipitated with the H/ACA families of snoRNAs. This family represents the conserved central region of Gar1. This region is necessary and sufficient for normal cell growth, and specifically binds two snoRNAs snR10 and snR30. This region is also necessary for nucleolar targeting, and it is thought that the protein is co-transported to the nucleolus as part of a nucleoprotein complex [2]. In humans, Gar1 is also component of telomerase in vivo [3]. Naf1 is an essential protein that plays a role in ribosome biogenesis, modification of spliceosomal small nuclear RNAs and telomere synthesis, and is homologous to Gar1 [4].	Domain
B [auth A]	PF08068	DKCLD (NUC011) domain (DKCLD)	DKCLD (NUC011) domain	This is a TruB_N/PUA domain associated N-terminal domain of Dyskerin-like proteins [1].	Domain
B [auth A]	PF16198	tRNA pseudouridylate synthase B C-terminal domain (TruB_C_2)	tRNA pseudouridylate synthase B C-terminal domain	-	Family
B [auth A]	PF01509	TruB family pseudouridylate synthase (N terminal domain) (TruB_N)	TruB family pseudouridylate synthase (N terminal domain)	Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes TruB, a pseudouridylate synthase that specifically converts uracil 55 to pseudouridine in m ...	Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes TruB, a pseudouridylate synthase that specifically converts uracil 55 to pseudouridine in most tRNAs. This family also includes Cbf5p that modifies rRNA [2].	Domain
B [auth A]	PF01472	PUA domain (PUA)	PUA domain	The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modificatio ...	The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was detected also in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in the regulation of the expression of other genes [1]. It is predicted that the PUA domain is an RNA binding domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth 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
D [auth C]	Ribosome biogenesis protein Nop10	RNA binding binding snoRNA binding nucleic acid binding	ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process cellular component organization or biogenesis RNA processing rRNA metabolic process pseudouridine synthesis RNA modification macromolecule modification	protein-containing complex ribonucleoprotein complex
C [auth B]	Small nucleolar rnp similar to gar1	-	pseudouridine synthesis nucleobase-containing compound metabolic process RNA modification macromolecule modification RNA metabolic process metabolic process cellular process primary metabolic process macromolecule metabolic process nucleic acid metabolic process cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular component organization or biogenesis	-
B [auth A]	Probable tRNA pseudouridine synthase B	RNA binding binding nucleic acid binding isomerase activity tRNA pseudouridine synthase activity catalytic activity, acting on RNA tRNA pseudouridine(55) synthase activity catalytic activity, acting on a nucleic acid pseudouridine synthase activity catalytic activity, acting on a tRNA catalytic activity intramolecular transferase activity	ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process pseudouridine synthesis rRNA pseudouridine synthesis ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process pseudouridine synthesis rRNA pseudouridine synthesis primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA modification biosynthetic process macromolecule modification metabolic process cellular process macromolecule metabolic process snRNA modification snRNA pseudouridine synthesis snRNA metabolic process snRNA processing mRNA modification mRNA metabolic process mRNA pseudouridine synthesis box H/ACA sno(s)RNA 3'-end processing sno(s)RNA processing sno(s)RNA 3'-end processing box H/ACA sno(s)RNA processing box H/ACA sno(s)RNA metabolic process sno(s)RNA metabolic process RNA 3'-end processing tRNA pseudouridine synthesis tRNA modification tRNA metabolic process tRNA processing	-
A [auth E]	H/ACA RNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth D]	IPR050257	Large ribosomal subunit protein eL8/uL1-like	Family
E [auth D]	IPR004038	Ribosomal protein eL8/eL30/eS12/Gadd45	Domain
E [auth D]	IPR022481	Large ribosomal subunit protein eL8, archaea	Family
E [auth D]	IPR004037	Large ribosomal subunit protein eL8-like, conserved site	Conserved Site
E [auth D]	IPR029064	Ribosomal protein eL30-like superfamily	Homologous Superfamily
E [auth D]	IPR018492	Ribosomal protein eL8/Nhp2 family	Family
D [auth C]	IPR023532	H/ACA ribonucleoprotein complex subunit Nop10 , archaeal-type	Family
D [auth C]	IPR007264	H/ACA ribonucleoprotein complex, subunit Nop10	Family
D [auth C]	IPR036756	H/ACA ribonucleoprotein complex, subunit Nop10 superfamily	Homologous Superfamily
C [auth B]	IPR038664	H/ACA RNP complex subunit Gar1/Naf1, Cbf5-binding domain	Homologous Superfamily
C [auth B]	IPR007504	H/ACA ribonucleoprotein complex, subunit Gar1/Naf1	Family
C [auth B]	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
B [auth A]	IPR015947	PUA-like superfamily	Homologous Superfamily
B [auth A]	IPR020103	Pseudouridine synthase, catalytic domain superfamily	Homologous Superfamily
B [auth A]	IPR004521	Uncharacterised domain CHP00451	Domain
B [auth A]	IPR002501	Pseudouridine synthase II, N-terminal	Domain
B [auth A]	IPR026326	Probable tRNA pseudouridine synthase B, archaeal	Family
B [auth A]	IPR032819	tRNA pseudouridylate synthase B, C-terminal	Domain
B [auth A]	IPR036974	PUA domain superfamily	Homologous Superfamily
B [auth A]	IPR012960	Dyskerin-like	Domain
B [auth A]	IPR002478	PUA domain	Domain
B [auth A]	IPR004802	tRNA pseudouridine synthase B family	Family