2RFK | pdb_00002rfk

Substrate RNA Positioning in the Archaeal H/ACA Ribonucleoprotein Complex

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)
F [auth C]	d2rfkc_	All beta proteins	Reductase/isomerase/elongation factor common domain	Translation proteins	Gar1-like SnoRNP	Gar1 homolog PF1791	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
E [auth B]	d2rfkb_	Small proteins	Rubredoxin-like	Nop10-like SnoRNP	Nucleolar RNA-binding protein Nop10-like	Ribosome biogenesis protein Nop10	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
D [auth A]	d2rfka1	All beta proteins	PUA domain-like	PUA domain-like	automated matches	automated matches	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
D [auth A]	d2rfka2	Alpha and beta proteins (a+b)	Pseudouridine synthase	Pseudouridine synthase	Pseudouridine synthase II TruB	automated matches	(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)
F [auth C]	SCOP2B Superfamily	Translational proteins	8040331	3000811	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	Nop10-like SnoRNP Znf-like	8040332	3000486	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	Pseudouridine synthase	8040330	3001360	SCOP2B (2022-06-29)
D [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)
F [auth C]	Gar1	e2rfkC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Gar1	ECOD (1.6)
E [auth B]	Nop10p	e2rfkB1	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)
D [auth A]	PUA	e2rfkA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: PUA	ECOD (1.6)
D [auth A]	TruB_N	e2rfkA2	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)
F [auth C]	2.40.10.230	Mainly Beta	Beta Barrel	Thrombin, subunit H	Probable tRNA pseudouridine synthase domain	CATH (4.3.0)
E [auth B]	2.20.28.40	Mainly Beta	Single Sheet	Rubrerythrin, domain 2	H/ACA ribonucleoprotein complex, subunit Nop10	CATH (4.3.0)
D [auth A]	2.30.130.10	Mainly Beta	Roll	Archaeosine Trna-guanine Transglycosylase	Chain: A, domain 4	CATH (4.3.0)
D [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
F [auth C]	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
E [auth B]	PF04135	Nucleolar RNA-binding protein, Nop10p family (Nop10p)	Nucleolar RNA-binding protein, Nop10p family	-	Family
D [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
D [auth A]	PF16198	tRNA pseudouridylate synthase B C-terminal domain (TruB_C_2)	tRNA pseudouridylate synthase B C-terminal domain	-	Family
D [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
D [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
F [auth C]	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	-
E [auth B]	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
D [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	-
C [auth F]	target RNA	-	-	-
B [auth E]	guide RNA 2	-	-	-
A [auth D]	guide RNA 1	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F [auth C]	IPR038664	H/ACA RNP complex subunit Gar1/Naf1, Cbf5-binding domain	Homologous Superfamily
F [auth C]	IPR007504	H/ACA ribonucleoprotein complex, subunit Gar1/Naf1	Family
F [auth C]	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
E [auth B]	IPR023532	H/ACA ribonucleoprotein complex subunit Nop10 , archaeal-type	Family
E [auth B]	IPR007264	H/ACA ribonucleoprotein complex, subunit Nop10	Family
E [auth B]	IPR036756	H/ACA ribonucleoprotein complex, subunit Nop10 superfamily	Homologous Superfamily
D [auth A]	IPR015947	PUA-like superfamily	Homologous Superfamily
D [auth A]	IPR020103	Pseudouridine synthase, catalytic domain superfamily	Homologous Superfamily
D [auth A]	IPR004521	Uncharacterised domain CHP00451	Domain
D [auth A]	IPR002501	Pseudouridine synthase II, N-terminal	Domain
D [auth A]	IPR026326	Probable tRNA pseudouridine synthase B, archaeal	Family
D [auth A]	IPR032819	tRNA pseudouridylate synthase B, C-terminal	Domain
D [auth A]	IPR036974	PUA domain superfamily	Homologous Superfamily
D [auth A]	IPR012960	Dyskerin-like	Domain
D [auth A]	IPR002478	PUA domain	Domain
D [auth A]	IPR004802	tRNA pseudouridine synthase B family	Family

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.