Annotations: 8YF5

Cryo EM structure of Komagataella phaffii 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	LRR_1, LRR_5, LRR_6, LRR_8	e8yf5A01	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: LRR_1, LRR_5, LRR_6, LRR_8	ECOD (v294.2)
B	LRR_1, LRR_5, LRR_6, LRR_8	e8yf5B01	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: LRR_1, LRR_5, LRR_6, LRR_8	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	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
E	PF04818	CID domain (CID)	CID domain	-	Repeat
B, D	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, C	5'-3' exoribonuclease	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	nuclear RNA surveillance catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA surveillance nuclear polyadenylation-dependent rRNA catabolic process nuclear RNA surveillance catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA surveillance nuclear polyadenylation-dependent rRNA catabolic process RNA catabolic process RNA splicing gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA processing 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 NAD-cap decapping RNA decapping transcription elongation by RNA polymerase II regulation of cellular process negative regulation of biological process 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 cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of DNA-templated transcription elongation negative regulation of DNA-templated transcription regulation of biological process regulation of transcription elongation by RNA polymerase II negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process negative regulation of DNA-templated transcription, elongation regulation of gene expression DNA-templated transcription elongation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process mRNA catabolic process nuclear-transcribed mRNA catabolic process nuclear mRNA surveillance negative regulation of gene expression termination of RNA polymerase II transcription, exosome-dependent sno(s)RNA processing sno(s)RNA metabolic process 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 cellular component organization or biogenesis positive regulation of protein-containing complex disassembly positive regulation of cellular process protein-containing complex organization positive regulation of RNA biosynthetic process 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 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	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex RNA polymerase II termination complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle exoribonuclease complex transferase complex endonuclease complex membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex RNA polymerase II termination complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle exoribonuclease complex transferase complex endonuclease complex protein kinase complex transferase complex, transferring phosphorus-containing groups Las1 complex endoribonuclease complex cytoplasm cytosol intracellular protein-containing complex
E	Exonuclease Rat1p and Rai1p interacting protein	hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exonuclease activity catalytic activity RNA polymerase binding protein binding binding RNA polymerase II complex binding RNA polymerase II C-terminal domain binding RNA polymerase core enzyme binding enzyme 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	-
B, D	Decapping nuclease	phosphodiesterase decapping endonuclease activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity catalytic activity binding nucleoside phosphate binding nucleotide binding phosphodiesterase decapping endonuclease activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity catalytic activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding pyrophosphatase activity mRNA 5'-diphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides enzyme regulator activity molecular function regulator activity RNA binding nucleic acid binding cation binding ion binding metal ion binding	nuclear RNA surveillance catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA surveillance nuclear polyadenylation-dependent rRNA catabolic process nuclear RNA surveillance catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA surveillance nuclear polyadenylation-dependent rRNA catabolic process RNA catabolic process termination of RNA polymerase II transcription, poly(A)-coupled nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription termination RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process termination of RNA polymerase II transcription regulation of cellular process negative regulation of biological process deadenylation-independent decapping of nuclear-transcribed mRNA negative regulation of cellular process mRNA methylguanosine-cap decapping nuclear-transcribed mRNA catabolic process, deadenylation-independent decay 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 regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process RNA decapping NAD-cap decapping 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 cellular component organization or biogenesis 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 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 RNA processing 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	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex RNA polymerase II termination complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle exoribonuclease complex transferase complex endonuclease complex membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex RNA polymerase II termination complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle exoribonuclease complex transferase complex endonuclease complex protein kinase complex transferase complex, transferring phosphorus-containing groups Las1 complex endoribonuclease complex cytoplasm cytosol intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR027073	5'-3' exoribonuclease	Family
A, C	IPR041412	Xrn1, helical domain	Domain
A, C	IPR004859	Xrn1, N-terminal	Domain
A, C	IPR017151	5'-3' exoribonuclease type 2	Family
E	IPR006569	CID domain	Domain
E	IPR008942	ENTH/VHS	Homologous Superfamily
E	IPR047883	Regulator of Ty1 transposition protein 103-like, CID domain	Domain
B, D	IPR039039	RAI1-like family	Family
B, D	IPR013961	RAI1-like	Domain

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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.

8YF5 | pdb_00008yf5

Cryo EM structure of Komagataella phaffii 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