2ROK | pdb_00002rok

Solution structure of the cap-binding domain of PARN complexed with the cap analog

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
A	d2roka1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d2roka3	Artifacts	Tags	Tags	Tags	C-terminal Tags	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d2roka2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	RNA-binding domain, RBD	8043557	3000110	SCOP2B (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	e2rokA1	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)

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	cation binding ion binding binding small molecule binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA exonuclease activity, producing 5'-phosphomonoesters 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity poly(A)-specific ribonuclease activity hydrolase activity, acting on ester bonds cation binding ion binding binding small molecule binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA exonuclease activity, producing 5'-phosphomonoesters 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity poly(A)-specific ribonuclease activity hydrolase activity, acting on ester bonds nuclease activity exonuclease activity catalytic activity RNA binding nucleic acid binding metal ion binding	sno(s)RNA processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process sno(s)RNA 3'-end processing biosynthetic process sno(s)RNA metabolic process RNA 3'-end processing sno(s)RNA processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process sno(s)RNA 3'-end processing biosynthetic process sno(s)RNA metabolic process RNA 3'-end processing metabolic process cellular process RNA processing macromolecule metabolic process poly(A)-dependent snoRNA 3'-end processing regulation of cellular process negative regulation of biological process regulation of primary metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of biological process negative regulation of metabolic process positive regulation of mRNA metabolic process nucleobase-containing compound catabolic process nuclear-transcribed mRNA poly(A) tail shortening positive regulation of RNA metabolic process regulation of gene expression negative regulation of gene expression negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process regulation of metabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process positive regulation of biological process macromolecule catabolic process mRNA destabilization regulation of mRNA catabolic process negative regulation of cellular process positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process nuclear-transcribed mRNA catabolic process RNA destabilization biological regulation regulation of macromolecule metabolic process regulation of catabolic process 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 RNA stability regulation of mRNA metabolic process miRNA catabolic process miRNA metabolic process box H/ACA sno(s)RNA 3'-end processing box H/ACA sno(s)RNA processing box H/ACA sno(s)RNA metabolic process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	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 cytoplasm

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	IPR034042	PARN, R3H domain	Domain
A	IPR051181	CAF1 family poly(A)-specific ribonucleases	Family
A	IPR036867	R3H domain superfamily	Homologous Superfamily
A	IPR001374	R3H domain	Domain
A	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A	IPR006941	Ribonuclease CAF1	Family
A	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
A	IPR012337	Ribonuclease H-like 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 R01GM157729.