3U28 | pdb_00003u28

Crystal structure of a Cbf5-Nop10-Gar1 complex from Saccharomyces cerevisiae

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
B	d3u28b_	Small proteins	Rubredoxin-like	Nop10-like SnoRNP	Nucleolar RNA-binding protein Nop10-like	H/aca ribonucleoprotein complex subunit 3	yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	Gar1	e3u28C1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Gar1	ECOD (1.6)
B	Nop10p	e3u28B1	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)
A	PUA	e3u28A3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: PUA	ECOD (1.6)
A	TruB_N	e3u28A4	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)
C	2.40.10.230	Mainly Beta	Beta Barrel	Thrombin, subunit H	Probable tRNA pseudouridine synthase domain	CATH (4.3.0)
B	4.10.80.300	Few Secondary Structures	Irregular	Rhinovirus 14, subunit 4		CATH (4.3.0)
A	2.30.130.10	Mainly Beta	Roll	Archaeosine Trna-guanine Transglycosylase	Chain: A, domain 4	CATH (4.3.0)
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
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
B	PF04135	Nucleolar RNA-binding protein, Nop10p family (Nop10p)	Nucleolar RNA-binding protein, Nop10p family	-	Family
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
A	PF16198	tRNA pseudouridylate synthase B C-terminal domain (TruB_C_2)	tRNA pseudouridylate synthase B C-terminal domain	-	Family
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
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
C	H/ACA ribonucleoprotein complex subunit 1	RNA binding binding snoRNA binding nucleic acid binding box H/ACA snoRNA binding	pseudouridine synthesis snRNA modification snRNA pseudouridine synthesis RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification snRNA metabolic process biosynthetic process pseudouridine synthesis snRNA modification snRNA pseudouridine synthesis RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification snRNA metabolic process biosynthetic process macromolecule modification snRNA processing metabolic process cellular process macromolecule metabolic process RNA processing ribonucleoprotein complex biogenesis rRNA processing rRNA modification cellular component biogenesis ribosome biogenesis cellular component organization or biogenesis rRNA metabolic process rRNA pseudouridine synthesis snoRNA guided rRNA pseudouridine synthesis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen protein-containing complex catalytic complex sno(s)RNA-containing ribonucleoprotein complex nuclear protein-containing complex box H/ACA snoRNP complex box H/ACA RNP complex ribonucleoprotein complex
B	H/ACA ribonucleoprotein complex subunit 3	RNA binding binding snoRNA binding nucleic acid binding telomerase RNA binding	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 snoRNA guided rRNA pseudouridine synthesis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen protein-containing complex sno(s)RNA-containing ribonucleoprotein complex ribonucleoprotein complex catalytic complex nuclear protein-containing complex box H/ACA snoRNP complex box H/ACA RNP complex
A	H/ACA ribonucleoprotein complex subunit 4	isomerase activity snRNA pseudouridine synthase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid pseudouridine synthase activity catalytic activity intramolecular transferase activity DNA binding binding nucleic acid binding RNA binding mRNA binding	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 primary metabolic process gene expression 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 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 cell division pseudouridine synthesis rRNA pseudouridine synthesis snoRNA guided rRNA 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 snRNA modification snRNA pseudouridine synthesis snRNA metabolic process snRNA processing mRNA modification mRNA metabolic process mRNA pseudouridine synthesis	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle chromosome, centromeric region intracellular membraneless organelle chromosome chromosomal region cytoplasm 90S preribosome preribosome protein-containing complex ribonucleoprotein complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle chromosome, centromeric region intracellular membraneless organelle chromosome chromosomal region cytoplasm 90S preribosome preribosome protein-containing complex ribonucleoprotein complex membrane-bounded organelle catalytic complex sno(s)RNA-containing ribonucleoprotein complex nucleus membrane-enclosed lumen nuclear protein-containing complex box H/ACA snoRNP complex intracellular membrane-bounded organelle nucleolus intracellular organelle lumen box H/ACA RNP complex organelle lumen nuclear lumen polymeric cytoskeletal fiber cytoskeleton supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton

InterPro: Protein Family Classification InterPro Database Homepage

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

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.