Annotations: 3FQD

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	XRN2-like	8051181	4007229	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	5' to 3' exonuclease C-terminal subdomain	8105318	3000537	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PIN domain-like	8105317	3001041	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	PF03159	e3fqdA2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: PF03159	ECOD (1.6)
B	PF08652	e3fqdB1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: PF08652	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF17846	Xrn1 helical domain (XRN_M)	Xrn1 helical domain	This helical domain is part of the Xrn1 catalytic core [1]. Xrn1 is a cytoplasmic 5'-3' exonuclease that degrades decapped mRNAs.	Domain
A	PF03159	XRN 5'-3' exonuclease N-terminus (XRN_N)	XRN 5'-3' exonuclease N-terminus	-	Family
B	PF08652	RAI1 like PD-(D/E)XK nuclease (RAI1)	RAI1 like PD-(D/E)XK nuclease	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	5'-3' exoribonuclease 2	5'-3' RNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exonuclease activity catalytic activity RNA binding 5'-3' RNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exonuclease activity catalytic activity RNA binding binding organic cyclic compound binding nucleic acid binding	regulation of cellular process catabolic process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of cellular process catabolic process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process negative regulation of cellular biosynthetic process nucleic acid metabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process regulation of cellular biosynthetic process regulation of gene expression organic cyclic compound metabolic process negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process organic substance catabolic process tRNA metabolic process tRNA surveillance ncRNA metabolic process RNA surveillance tRNA decay nucleobase-containing compound biosynthetic process DNA-templated transcription termination RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process organic cyclic compound biosynthetic process nuclear RNA surveillance nuclear mRNA surveillance positive regulation of chromosome segregation regulation of chromosome segregation regulation of cell cycle process positive regulation of biological process positive regulation of cell cycle positive regulation of cell cycle process cell cycle regulation of cell cycle chromosome segregation positive regulation of cellular process cell cycle process mRNA processing RNA processing ribonucleoprotein complex biogenesis rRNA processing cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) cellular component biogenesis ribosome biogenesis cellular component organization or biogenesis rRNA metabolic process endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) maturation of 5.8S rRNA ribosomal large subunit biogenesis maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) maturation of LSU-rRNA	protein-containing complex intracellular anatomical structure catalytic complex cellular anatomical entity transferase complex endonuclease complex protein kinase complex transferase complex, transferring phosphorus-containing groups Las1 complex endoribonuclease complex cytoplasm cytosol exoribonuclease complex intracellular protein-containing complex protein-containing complex intracellular anatomical structure catalytic complex cellular anatomical entity transferase complex endonuclease complex protein kinase complex transferase complex, transferring phosphorus-containing groups Las1 complex endoribonuclease complex cytoplasm cytosol exoribonuclease complex intracellular protein-containing complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
B	Protein din1	guanyl nucleotide binding binding nucleotide binding GDP binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding guanyl nucleotide binding binding nucleotide binding GDP binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding phosphodiesterase decapping endonuclease activity endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity nuclease activity hydrolase activity, acting on ester bonds RNA endonuclease activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters catalytic activity RNA NAD+-cap (NAD+-forming) hydrolase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides pyrophosphatase activity mRNA 5'-diphosphatase activity 5'-hydroxyl dinucleotide hydrolase activity RNA binding nucleic acid binding cation binding metal ion binding	regulation of cellular process catabolic process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of cellular process catabolic process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process negative regulation of cellular biosynthetic process nucleic acid metabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process regulation of cellular biosynthetic process regulation of gene expression organic cyclic compound metabolic process negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process organic substance catabolic process NAD-cap decapping RNA decapping mRNA processing RNA processing	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex catalytic complex transferase complex endonuclease complex protein kinase complex transferase complex, transferring phosphorus-containing groups Las1 complex endoribonuclease complex exoribonuclease complex intracellular protein-containing complex intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex catalytic complex transferase complex endonuclease complex protein kinase complex transferase complex, transferring phosphorus-containing groups Las1 complex endoribonuclease complex exoribonuclease complex intracellular protein-containing complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR027073	5'-3' exoribonuclease	Family
A	IPR041412	Xrn1, helical domain	Domain
A	IPR004859	Xrn1, N-terminal	Domain
A	IPR017151	5'-3' exoribonuclease type 2	Family
B	IPR039039	RAI1-like family	Family
B	IPR013961	RAI1-like	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.