Annotations: 3U28

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)
A	PF01472	e3u28A3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: PF01472	ECOD (1.6)
A	PF01509,PF08068,PF16198	e3u28A4	A: a+b two layers	X: Alpha-beta plaits	H: Pseudouridine synthase (From Topology)	T: Pseudouridine synthase	F: PF01509,PF08068,PF16198	ECOD (1.6)
B	PF04135	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: PF04135	ECOD (1.6)
C	PF04410	e3u28C1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: PF04410	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
B	4.10.80.300	Few Secondary Structures	Irregular	Rhinovirus 14, subunit 4		CATH (4.3.0)
C	2.40.10.230	Mainly Beta	Beta Barrel	Thrombin, subunit H	Probable tRNA pseudouridine synthase domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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)	-	Family
A	PF01472	PUA domain (PUA)	PUA domain	-	Family
B	PF04135	Nucleolar RNA-binding protein, Nop10p family (Nop10p)	Nucleolar RNA-binding protein, Nop10p family	-	Family
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	H/ACA ribonucleoprotein complex subunit 4	DNA binding binding organic cyclic compound binding nucleic acid binding RNA binding mRNA binding isomerase activity pseudouridine synthase activity catalytic activity intramolecular transferase activity	ribonucleoprotein complex biogenesis cellular biosynthetic process RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis ribosome biogenesis organic substance metabolic process organic substance biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process cellular metabolic process ribonucleoprotein complex biogenesis cellular biosynthetic process RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis ribosome biogenesis organic substance metabolic process organic substance biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process RNA modification biosynthetic process macromolecule modification ncRNA metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process cell division pseudouridine synthesis rRNA pseudouridine synthesis snoRNA guided rRNA pseudouridine synthesis cell cycle snRNA modification snRNA pseudouridine synthesis snRNA metabolic process mRNA modification mRNA metabolic process mRNA pseudouridine synthesis box H/ACA sno(s)RNA processing sno(s)RNA metabolic process RNA 3'-end processing 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 metabolic process	intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromosome, centromeric region chromosome cellular anatomical entity chromosomal region non-membrane-bounded organelle cytoplasm 90S preribosome preribosome protein-containing complex ribonucleoprotein complex intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromosome, centromeric region chromosome cellular anatomical entity chromosomal region non-membrane-bounded organelle 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
B	H/ACA ribonucleoprotein complex subunit 3	RNA binding binding organic cyclic compound binding snoRNA binding nucleic acid binding telomerase RNA binding	ribonucleoprotein complex biogenesis cellular biosynthetic process RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis ribosome biogenesis organic substance metabolic process organic substance biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process pseudouridine synthesis ribonucleoprotein complex biogenesis cellular biosynthetic process RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis ribosome biogenesis organic substance metabolic process organic substance biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process pseudouridine synthesis rRNA pseudouridine synthesis cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process RNA modification biosynthetic process macromolecule modification ncRNA metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process snRNA modification snRNA pseudouridine synthesis snRNA metabolic process snoRNA guided rRNA pseudouridine synthesis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle 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
C	H/ACA ribonucleoprotein complex subunit 1	RNA binding binding organic cyclic compound binding snoRNA binding nucleic acid binding box H/ACA snoRNA binding	pseudouridine synthesis snRNA modification snRNA pseudouridine synthesis RNA metabolic process primary metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process RNA modification organic substance metabolic process snRNA metabolic process macromolecule modification ncRNA metabolic process nucleic acid catabolic process pseudouridine synthesis snRNA modification snRNA pseudouridine synthesis RNA metabolic process primary metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process RNA modification organic substance metabolic process snRNA metabolic process macromolecule modification ncRNA metabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process ribonucleoprotein complex biogenesis cellular biosynthetic process rRNA processing rRNA modification cellular component biogenesis ribosome biogenesis organic substance biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process rRNA pseudouridine synthesis cellular metabolic process snoRNA guided rRNA pseudouridine synthesis gene expression macromolecule biosynthetic process biosynthetic process cellular process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
B	IPR007264	H/ACA ribonucleoprotein complex, subunit Nop10	Family
B	IPR036756	H/ACA ribonucleoprotein complex, subunit Nop10 superfamily	Homologous Superfamily
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

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 R01GM133198.