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	PIN domain-like	8105317	3001041	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	5' to 3' exonuclease, C-terminal subdomain	8105318	3000537	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)
B		e3fqdB1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: NusG	F:	ECOD (20:10:01)
A		e3fqdA2	A: Suppressor of Fused, C-terminal domain	X: HTH	H: HLH, helix-loop-helix DNA-binding domain	T: HLH	F:	ECOD (20:10:01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF08652	RAI1 like PD-(D/E)XK nuclease (RAI1)	RAI1 like PD-(D/E)XK nuclease	-	Family
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Protein din1	RNA NAD+-cap (NAD+-forming) hydrolase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity guanyl nucleotide binding binding nucleotide binding GDP binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding RNA NAD+-cap (NAD+-forming) hydrolase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity guanyl nucleotide binding binding nucleotide binding GDP binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide 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, hydrolytic mechanism RNA nuclease activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity pyrophosphatase activity mRNA 5'-diphosphatase activity 5'-hydroxyl dinucleotide hydrolase activity RNA exonuclease activity exonuclease activity RNA binding nucleic acid binding cation binding metal ion binding	regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic 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 negative regulation of metabolic process regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic 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 negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of gene expression 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 NAD-cap decapping RNA decapping nucleobase-containing compound biosynthetic process mRNA processing RNA biosynthetic process nucleic acid biosynthetic process 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	cellular anatomical structure intracellular anatomical structure cytoplasm 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 cellular anatomical structure intracellular anatomical structure cytoplasm 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
A	5'-3' exoribonuclease 2	5'-3' RNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA exonuclease activity, producing 5'-phosphomonoesters RNA exonuclease activity RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity exonuclease activity catalytic activity RNA binding binding 5'-3' RNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA exonuclease activity, producing 5'-phosphomonoesters RNA exonuclease activity RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity exonuclease activity catalytic activity RNA binding binding nucleic acid binding	regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic 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 negative regulation of metabolic process regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic 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 negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of gene expression 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 rapid tRNA decay tRNA metabolic process tRNA surveillance RNA surveillance tRNA decay nucleobase-containing compound biosynthetic process DNA-templated transcription termination RNA biosynthetic process DNA-templated transcription nucleic acid 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 transferase complex endonuclease complex protein kinase complex transferase complex, transferring phosphorus-containing groups Las1 complex cellular anatomical structure endoribonuclease complex cytoplasm cytosol exoribonuclease complex intracellular protein-containing complex protein-containing complex intracellular anatomical structure catalytic complex transferase complex endonuclease complex protein kinase complex transferase complex, transferring phosphorus-containing groups Las1 complex cellular anatomical structure endoribonuclease complex cytoplasm cytosol 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
B	IPR039039	RAI1-like family	Family
B	IPR013961	RAI1-like	Domain
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

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.