Annotations: 9DSO

CRYO-EM STRUCTURE OF SACCHAROMYCES CEREVISIAE RAT1-RAI1-RTT103 COMPLEX

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	TIP49	e9dsoA01	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: TIP49	ECOD (v294.2)

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	Regulator of Ty1 transposition protein 103	DNA binding binding nucleic acid binding phosphoprotein binding RNA polymerase binding RNA polymerase II C-terminal domain binding enzyme binding RNA polymerase II C-terminal domain phosphoserine binding protein binding RNA polymerase II complex binding RNA polymerase core enzyme binding phosphoserine residue binding protein phosphorylated amino acid binding	mRNA 3'-end processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing mRNA 3'-end processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing metabolic process cellular process RNA processing macromolecule metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process retrotransposition regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process transposition regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process transposable element silencing regulation of macromolecule biosynthetic process regulation of metabolic process	intracellular organelle site of double-strand break cellular anatomical structure intracellular anatomical structure organelle membraneless organelle site of DNA damage intracellular membraneless organelle chromosome chromatin membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B	Decapping nuclease RAI1	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 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 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 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 binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding pyrophosphatase activity mRNA 5'-diphosphatase activity enzyme regulator activity molecular function regulator activity RNA binding nucleic acid binding cation binding ion binding metal ion binding	maturation of 5.8S rRNA ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) maturation of 5.8S rRNA ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) biosynthetic process metabolic process cellular process macromolecule metabolic process cellular component organization or biogenesis RNA processing rRNA metabolic process regulation of cellular process catabolic process negative regulation of biological process macromolecule catabolic 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 regulation of macromolecule metabolic process mRNA metabolic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process regulation of metabolic process ribosomal large subunit biogenesis maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) maturation of LSU-rRNA nuclear RNA surveillance RNA surveillance nuclear polyadenylation-dependent rRNA catabolic process termination of RNA polymerase II transcription, poly(A)-coupled DNA-templated transcription termination DNA-templated transcription transcription by RNA polymerase II termination of RNA polymerase II transcription deadenylation-independent decapping of nuclear-transcribed mRNA mRNA methylguanosine-cap decapping nuclear-transcribed mRNA catabolic process, deadenylation-independent decay RNA decapping NAD-cap decapping mRNA processing protein-containing complex disassembly regulation of protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process cellular component disassembly positive regulation of RNA metabolic process regulation of termination of DNA-templated transcription regulation of DNA-templated transcription regulation of termination of RNA polymerase II transcription regulation of cellular component organization positive regulation of cellular component organization positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of termination of DNA-templated transcription cellular component organization positive regulation of biosynthetic process positive regulation of termination of RNA polymerase II transcription positive regulation of protein-containing complex disassembly positive regulation of cellular process regulation of RNA biosynthetic process protein-containing complex organization positive regulation of RNA biosynthetic process cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex catalytic complex RNA polymerase II termination complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle organelle exoribonuclease complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex catalytic complex RNA polymerase II termination complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle organelle exoribonuclease complex transferase complex endonuclease complex protein kinase complex transferase complex, transferring phosphorus-containing groups Las1 complex endoribonuclease complex intracellular protein-containing complex
A	5'-3' exoribonuclease 2	RNA binding binding rRNA binding nucleic acid 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 RNA binding binding rRNA binding nucleic acid 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 mRNA 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 termination of RNA polymerase II transcription, poly(A)-coupled nucleobase-containing compound biosynthetic process DNA-templated transcription termination RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II termination of RNA polymerase II transcription NAD-cap decapping RNA decapping transcription elongation by RNA polymerase II negative regulation of transcription elongation by RNA polymerase II regulation of primary metabolic process negative regulation of RNA biosynthetic process regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription elongation negative regulation of DNA-templated transcription regulation of transcription elongation by RNA polymerase II negative regulation of DNA-templated transcription, elongation DNA-templated transcription elongation regulation of DNA-templated transcription negative regulation of RNA metabolic process ribonucleoprotein complex biogenesis rRNA processing cellular component biogenesis ribosome biogenesis cellular component organization or biogenesis RNA processing rRNA metabolic process RNA surveillance nuclear RNA surveillance nuclear mRNA surveillance sno(s)RNA processing sno(s)RNA metabolic process nuclear polyadenylation-dependent rRNA catabolic process RNA splicing mRNA processing RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile termination of RNA polymerase II transcription, exosome-dependent protein-containing complex disassembly regulation of protein-containing complex disassembly positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process cellular component disassembly positive regulation of RNA metabolic process regulation of termination of DNA-templated transcription regulation of termination of RNA polymerase II transcription regulation of cellular component organization positive regulation of cellular component organization positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of termination of DNA-templated transcription cellular component organization positive regulation of biosynthetic process positive regulation of termination of RNA polymerase II transcription positive regulation of protein-containing complex disassembly positive regulation of cellular process protein-containing complex organization positive regulation of RNA biosynthetic process cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) 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	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex catalytic complex RNA polymerase II termination complex nuclear protein-containing complex exoribonuclease complex transferase complex endonuclease complex protein kinase complex transferase complex, transferring phosphorus-containing groups Las1 complex endoribonuclease complex cytosol intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR006569	CID domain	Domain
C	IPR008942	ENTH/VHS	Homologous Superfamily
C	IPR047883	Regulator of Ty1 transposition protein 103-like, CID domain	Domain
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

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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.

9DSO | pdb_00009dso

CRYO-EM STRUCTURE OF SACCHAROMYCES CEREVISIAE RAT1-RAI1-RTT103 COMPLEX

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage