3CTR

Crystal structure of the RRM-domain of the poly(A)-specific ribonuclease PARN bound to m7GTP

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Canonical RBD	8087512	4000236	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RNA-binding domain RBD	8087513	3000110	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF08675	e3ctrA1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: PF08675	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF08675	RNA binding domain (RNA_bind)	RNA binding domain	This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Poly(A)-specific ribonuclease PARN	nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity cation binding ion binding binding small molecule binding mRNA 3'-UTR binding RNA binding organic cyclic compound binding nucleic acid binding mRNA binding telomerase RNA binding nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity cation binding ion binding binding small molecule binding mRNA 3'-UTR binding RNA binding organic cyclic compound binding nucleic acid binding mRNA binding telomerase RNA binding protein binding kinase binding enzyme binding protein kinase binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity poly(A)-specific ribonuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters exonuclease activity metal ion binding	cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process sno(s)RNA metabolic process organic substance biosynthetic process RNA 3'-end processing RNA processing poly(A)-dependent snoRNA 3'-end processing sno(s)RNA processing cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process sno(s)RNA metabolic process organic substance biosynthetic process RNA 3'-end processing RNA processing poly(A)-dependent snoRNA 3'-end processing sno(s)RNA processing cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process sno(s)RNA 3'-end processing biosynthetic process ncRNA metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process regulation of cellular process negative regulation of biological process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process telomerase RNA stabilization negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process regulation of biological process negative regulation of metabolic process regulation of cellular metabolic process nucleobase-containing compound catabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process negative regulation of RNA metabolic process catabolic process macromolecule catabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process regulation of biosynthetic process biological regulation negative regulation of RNA catabolic process regulation of macromolecule metabolic process regulation of catabolic process organic cyclic compound catabolic process regulation of cellular biosynthetic process RNA stabilization regulation of RNA stability organic substance catabolic process negative regulation of cellular metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process mRNA catabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of mRNA metabolic process negative regulation of cellular biosynthetic process nuclear-transcribed mRNA poly(A) tail shortening positive regulation of RNA metabolic process negative regulation of gene expression negative regulation of macromolecule biosynthetic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay positive regulation of biological process mRNA destabilization regulation of mRNA catabolic process negative regulation of cellular process nuclear-transcribed mRNA catabolic process RNA destabilization mRNA metabolic process positive regulation of catabolic process regulation of mRNA stability negative regulation of biosynthetic process positive regulation of mRNA catabolic process regulation of mRNA metabolic process miRNA catabolic process miRNA metabolic process sexual reproduction reproductive process multicellular organismal reproductive process female gamete generation gamete generation regulation of catalytic activity regulation of transferase activity regulation of DNA biosynthetic process positive regulation of macromolecule biosynthetic process DNA metabolic process regulation of molecular function positive regulation of DNA metabolic process organic cyclic compound biosynthetic process DNA biosynthetic process regulation of DNA metabolic process regulation of telomerase activity positive regulation of cellular metabolic process nucleic acid biosynthetic process positive regulation of molecular function positive regulation of biosynthetic process positive regulation of cellular process positive regulation of telomerase activity positive regulation of transferase activity positive regulation of catalytic activity positive regulation of DNA biosynthetic process nucleobase-containing compound biosynthetic process positive regulation of cellular biosynthetic process positive regulation of organelle organization telomere organization RNA-templated DNA biosynthetic process telomere maintenance via telomere lengthening positive regulation of telomere maintenance via telomere lengthening positive regulation of telomere maintenance regulation of chromosome organization regulation of telomere maintenance via telomere lengthening regulation of organelle organization positive regulation of chromosome organization telomere maintenance positive regulation of telomere maintenance via telomerase regulation of telomere maintenance regulation of cellular component organization positive regulation of cellular component organization cellular component organization cellular component organization or biogenesis telomere maintenance via telomerase chromosome organization regulation of telomere maintenance via telomerase organelle organization RNA modification macromolecule modification nuclear-transcribed mRNA catabolic process, nonsense-mediated decay RNA localization to nucleus regulation of localization 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 box H/ACA sno(s)RNA processing box H/ACA sno(s)RNA 3'-end processing box H/ACA sno(s)RNA metabolic 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 nuclear speck nuclear body nucleoplasm cytoplasm cytosol synapse cell junction glutamatergic synapse postsynapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR014789	Poly(A)-specific ribonuclease, RNA-binding	Domain
A	IPR001374	R3H domain	Domain
A	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A	IPR034042	PARN, R3H domain	Domain
A	IPR036867	R3H domain superfamily	Homologous Superfamily
A	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A	IPR006941	Ribonuclease CAF1	Family
A	IPR035979	RNA-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O95453	dyskeratosis congenita idiopathic pulmonary fibrosis pulmonary fibrosis and/or bone marrow failure, Telomere-related, 4 dyskeratosis congenita, autosomal recessive 6 Hoyeraal-Hreidarsson syndrome acute interstitial pneumonia hematopoietic and lymphoid system neoplasm brain aneurysm intellectual disability diabetes mellitus Hamman-Rich syndrome idiopathic interstitial pneumonia ovarian cancer

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.