3CTR | pdb_00003ctr

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	RNA_bind	e3ctrA1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RNA_bind	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 catalytic activity, acting on a nucleic acid catalytic activity cation binding ion binding binding small molecule binding mRNA 3'-UTR binding RNA binding nucleic acid binding mRNA binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters nuclease activity catalytic activity, acting on a nucleic acid catalytic activity cation binding ion binding binding small molecule binding mRNA 3'-UTR binding RNA binding nucleic acid binding mRNA binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds exonuclease activity telomerase RNA binding protein binding kinase binding enzyme binding protein kinase binding poly(A)-specific ribonuclease activity metal ion binding	priRNA 3'-end processing regulation of cellular process negative regulation of biological process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process negative regulation of cellular process RNA 3'-end processing RNA processing regulatory ncRNA 3'-end processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process priRNA 3'-end processing regulation of cellular process negative regulation of biological process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process negative regulation of cellular process RNA 3'-end processing RNA processing regulatory ncRNA 3'-end processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process regulatory ncRNA processing regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process catabolic process macromolecule catabolic 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 negative regulation of catabolic process negative regulation of RNA catabolic process regulation of catabolic process nucleobase-containing compound catabolic process RNA stabilization regulation of RNA stability nucleic acid catabolic process negative regulation of RNA metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process mRNA catabolic process positive regulation of mRNA metabolic process nuclear-transcribed mRNA poly(A) tail shortening positive regulation of RNA metabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay positive regulation of biological process mRNA destabilization regulation of mRNA catabolic process positive regulation of cellular process nuclear-transcribed mRNA catabolic process RNA destabilization mRNA metabolic process positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process regulation of mRNA metabolic process miRNA catabolic process miRNA metabolic process 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 sexual reproduction reproductive process multicellular organismal reproductive process female gamete generation gamete generation positive regulation of organelle organization telomere organization regulation of DNA biosynthetic process positive regulation of macromolecule biosynthetic process RNA-templated DNA biosynthetic process telomere maintenance via telomere lengthening positive regulation of telomere maintenance via telomere lengthening positive regulation of telomere maintenance DNA metabolic process 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 DNA metabolic process positive regulation of telomere maintenance via telomerase DNA biosynthetic process regulation of DNA metabolic process regulation of telomere maintenance regulation of cellular component organization positive regulation of cellular component organization cellular component organization positive regulation of biosynthetic process cellular component organization or biogenesis telomere maintenance via telomerase chromosome organization positive regulation of DNA biosynthetic process regulation of telomere maintenance via telomerase organelle organization siRNA 3'-end processing RNA modification macromolecule modification poly(A)-dependent snoRNA 3'-end processing lncRNA processing 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	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 nuclear speck ribonucleoprotein granule nuclear body nucleoplasm supramolecular complex nuclear ribonucleoprotein granule 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	IPR051181	CAF1 family poly(A)-specific ribonucleases	Family
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 R01GM157729.