9YFM | pdb_00009yfm

insect H/ACA snoRNP class II composite

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], C [auth E]	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 C], E [auth G]	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 F], F [auth H]	PF04135	Nucleolar RNA-binding protein, Nop10p family (Nop10p)	Nucleolar RNA-binding protein, Nop10p family	-	Family
G [auth A], H [auth D]	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
G [auth A], H [auth D]	PF16198	tRNA pseudouridylate synthase B C-terminal domain (TruB_C_2)	tRNA pseudouridylate synthase B C-terminal domain	-	Family
G [auth A], H [auth D]	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
G [auth A], H [auth D]	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
A [auth B], C [auth E]	H/ACA ribonucleoprotein complex subunit	RNA binding binding snoRNA binding nucleic acid binding box H/ACA snoRNA 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 snoRNA guided 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	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex sno(s)RNA-containing ribonucleoprotein complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membraneless organelle box H/ACA snoRNP complex intracellular membrane-bounded organelle nucleolus intracellular organelle lumen box H/ACA RNP complex membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex sno(s)RNA-containing ribonucleoprotein complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membraneless organelle box H/ACA snoRNP complex intracellular membrane-bounded organelle nucleolus intracellular organelle lumen box H/ACA RNP complex intracellular organelle cellular anatomical structure organelle lumen organelle ribonucleoprotein complex membraneless organelle nuclear lumen
B [auth C], E [auth G]	H/ACA ribonucleoprotein complex subunit 2-like protein	RNA binding binding nucleic acid binding	-	protein-containing complex ribonucleoprotein complex
D [auth F], F [auth H]	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 RNA localization to nucleus regulation of localization regulation of biological process biological regulation positive regulation of biological process positive regulation of telomerase RNA localization to Cajal body telomerase RNA localization to Cajal body regulation of telomerase RNA localization to Cajal body localization telomerase RNA localization macromolecule localization RNA localization to Cajal body RNA localization	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex sno(s)RNA-containing ribonucleoprotein complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membraneless organelle box H/ACA snoRNP complex intracellular membrane-bounded organelle nucleolus intracellular organelle lumen box H/ACA RNP complex membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex sno(s)RNA-containing ribonucleoprotein complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membraneless organelle box H/ACA snoRNP complex intracellular membrane-bounded organelle nucleolus intracellular organelle lumen box H/ACA RNP complex intracellular organelle cellular anatomical structure organelle lumen organelle ribonucleoprotein complex membraneless organelle nuclear lumen
G [auth A], H [auth D]	H/ACA ribonucleoprotein complex subunit 4-like	isomerase activity pseudouridine synthase activity catalytic activity intramolecular transferase activity RNA binding binding nucleic acid 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 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	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex sno(s)RNA-containing ribonucleoprotein complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membraneless organelle box H/ACA snoRNP complex intracellular membrane-bounded organelle nucleolus intracellular organelle lumen box H/ACA RNP complex membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex sno(s)RNA-containing ribonucleoprotein complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membraneless organelle box H/ACA snoRNP complex intracellular membrane-bounded organelle nucleolus intracellular organelle lumen box H/ACA RNP complex intracellular organelle cellular anatomical structure organelle lumen organelle ribonucleoprotein complex membraneless organelle nuclear lumen
I	RNA (96-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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