4WFD

Structure of the Rrp6-Rrp47-Mtr4 interaction

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Rrp6-Rrp47 interacting regions-like	8055988	3002328	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Rrp6-Rrp47 interacting regions-like	8055988	3002328	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Rrp6-Rrp47 interacting regions-like	8055988	3002328	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Rrp6-Rrp47 interacting regions-like	8055987	3002328	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Rrp6-Rrp47 interacting regions-like	8055987	3002328	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	PF08066	e4wfdA1	A: extended segments	X: Exosome complex exonuclease RRP6 N-terminal domain (From Topology)	H: Exosome complex exonuclease RRP6 N-terminal domain (From Topology)	T: Exosome complex exonuclease RRP6 N-terminal domain	F: PF08066	ECOD (1.6)
D	PF08066	e4wfdD1	A: extended segments	X: Exosome complex exonuclease RRP6 N-terminal domain (From Topology)	H: Exosome complex exonuclease RRP6 N-terminal domain (From Topology)	T: Exosome complex exonuclease RRP6 N-terminal domain	F: PF08066	ECOD (1.6)
G	PF08066	e4wfdG1	A: extended segments	X: Exosome complex exonuclease RRP6 N-terminal domain (From Topology)	H: Exosome complex exonuclease RRP6 N-terminal domain (From Topology)	T: Exosome complex exonuclease RRP6 N-terminal domain	F: PF08066	ECOD (1.6)
B	PF04000	e4wfdB1	A: extended segments	X: Exosome complex protein LRP1 (From Topology)	H: Exosome complex protein LRP1 (From Topology)	T: Exosome complex protein LRP1	F: PF04000	ECOD (1.6)
E	PF04000	e4wfdE1	A: extended segments	X: Exosome complex protein LRP1 (From Topology)	H: Exosome complex protein LRP1 (From Topology)	T: Exosome complex protein LRP1	F: PF04000	ECOD (1.6)
H	PF04000	e4wfdH1	A: extended segments	X: Exosome complex protein LRP1 (From Topology)	H: Exosome complex protein LRP1 (From Topology)	T: Exosome complex protein LRP1	F: PF04000	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D, G	PF08066	PMC2NT (NUC016) domain (PMC2NT)	PMC2NT (NUC016) domain	This domain is found at the N-terminus of 3'-5' exonucleases with HRDC domains, and also in putative exosome components [1].	Domain
B, E, H	PF04000	Sas10/Utp3/C1D family (Sas10_Utp3)	Sas10/Utp3/C1D family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D, G	Exosome complex exonuclease RRP6	binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding RNA binding nucleic acid binding single-stranded RNA binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding RNA binding nucleic acid binding single-stranded RNA binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity 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 rRNA primary transcript binding rRNA binding	nuclear RNA surveillance catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process sno(s)RNA metabolic process ncRNA metabolic process nucleic acid catabolic process nuclear RNA surveillance catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process sno(s)RNA metabolic process ncRNA metabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process sno(s)RNA catabolic process RNA surveillance organic substance catabolic process RNA catabolic process nuclear polyadenylation-dependent snoRNA catabolic process cellular biosynthetic process organic substance biosynthetic process RNA 3'-end processing RNA processing poly(A)-dependent snoRNA 3'-end processing sno(s)RNA processing cellular metabolic process gene expression macromolecule biosynthetic process sno(s)RNA 3'-end processing biosynthetic process cellular process snRNA metabolic process snRNA processing U5 snRNA 3'-end processing snRNA 3'-end processing nuclear polyadenylation-dependent antisense transcript catabolic process antisense RNA transcript catabolic process antisense RNA metabolic process nuclear polyadenylation-dependent CUT catabolic process CUT metabolic process CUT catabolic process ribonucleoprotein complex biogenesis exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) rRNA processing cellular component biogenesis ribosome biogenesis cellular component organization or biogenesis rRNA metabolic process maturation of 5.8S rRNA maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) rRNA 3'-end processing snRNA catabolic process nuclear polyadenylation-dependent snRNA catabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process mRNA catabolic process regulation of biological process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process nuclear-transcribed mRNA catabolic process nuclear mRNA surveillance biological regulation regulation of macromolecule metabolic process mRNA metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process U4 snRNA 3'-end processing histone mRNA catabolic process histone mRNA metabolic process tRNA metabolic process TRAMP-dependent tRNA surveillance pathway tRNA surveillance tRNA decay nuclear polyadenylation-dependent rRNA catabolic process regulation of primary metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process nuclear polyadenylation-dependent mRNA catabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality positive regulation of nucleobase-containing compound metabolic process positive regulation of mRNA metabolic process positive regulation of RNA metabolic process polyadenylation-dependent mRNA catabolic process positive regulation of biological process mRNA destabilization regulation of mRNA catabolic process RNA destabilization regulation of catabolic process positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process cellular component organization organelle organization chromosome organization transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery U1 snRNA 3'-end processing	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle exosome (RNase complex) protein-containing complex catalytic complex exoribonuclease complex nuclear protein-containing complex nuclear exosome (RNase complex)
B, E, H	Exosome complex protein LRP1	DNA binding binding organic cyclic compound binding nucleic acid binding double-stranded DNA binding protein-containing complex binding RNA binding double-stranded RNA binding enzyme regulator activity molecular function regulator activity	cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process sno(s)RNA metabolic process organic substance biosynthetic process RNA 3'-end processing RNA processing poly(A)-dependent snoRNA 3'-end processing sno(s)RNA processing cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process sno(s)RNA metabolic process organic substance biosynthetic process RNA 3'-end processing RNA processing poly(A)-dependent snoRNA 3'-end processing sno(s)RNA processing cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process sno(s)RNA 3'-end processing biosynthetic process ncRNA metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process nuclear RNA surveillance catabolic process macromolecule catabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process RNA surveillance nuclear polyadenylation-dependent rRNA catabolic process organic substance catabolic process RNA catabolic process snRNA metabolic process snRNA processing U5 snRNA 3'-end processing snRNA 3'-end processing regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process nuclear polyadenylation-dependent CUT catabolic process CUT metabolic process CUT catabolic process cellular component organization organelle organization chromosome organization cellular component organization or biogenesis transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery ribonucleoprotein complex biogenesis exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) rRNA processing cellular component biogenesis ribosome biogenesis rRNA metabolic process maturation of 5.8S rRNA maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) rRNA 3'-end processing negative regulation of biological process negative regulation of cellular metabolic process mRNA catabolic process negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of gene expression negative regulation of macromolecule biosynthetic process negative regulation of cellular process negative regulation of macromolecule metabolic process nuclear-transcribed mRNA catabolic process nuclear mRNA surveillance mRNA metabolic process negative regulation of biosynthetic process U4 snRNA 3'-end processing	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle exosome (RNase complex) protein-containing complex catalytic complex exoribonuclease complex
C, F, I	ATP-dependent RNA helicase DOB1	oxidoreductase activity catalytic activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity 3'-5' RNA helicase activity RNA helicase activity ATP-dependent activity, acting on RNA ATP-dependent activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding oxidoreductase activity catalytic activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity 3'-5' RNA helicase activity RNA helicase activity ATP-dependent activity, acting on RNA ATP-dependent activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding RNA binding mRNA binding poly(A) binding poly-purine tract binding single-stranded RNA binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides	cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process sno(s)RNA metabolic process organic substance biosynthetic process RNA 3'-end processing RNA processing poly(A)-dependent snoRNA 3'-end processing sno(s)RNA processing cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process sno(s)RNA metabolic process organic substance biosynthetic process RNA 3'-end processing RNA processing poly(A)-dependent snoRNA 3'-end processing sno(s)RNA processing cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process sno(s)RNA 3'-end processing biosynthetic process ncRNA metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process snRNA metabolic process snRNA processing U5 snRNA 3'-end processing snRNA 3'-end processing ribonucleoprotein complex biogenesis exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) rRNA processing cellular component biogenesis ribosome biogenesis cellular component organization or biogenesis rRNA metabolic process maturation of 5.8S rRNA maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) rRNA 3'-end processing regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process RNA catabolic process mRNA catabolic process nuclear RNA surveillance regulation of biological process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process catabolic process macromolecule catabolic process negative regulation of cellular process RNA surveillance negative regulation of macromolecule metabolic process regulation of biosynthetic process nuclear-transcribed mRNA catabolic process nuclear mRNA surveillance biological regulation regulation of macromolecule metabolic process mRNA metabolic process organic cyclic compound catabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process organic substance catabolic process U4 snRNA 3'-end processing mRNA processing nuclear mRNA surveillance of mRNA 3'-end processing tRNA metabolic process TRAMP-dependent tRNA surveillance pathway tRNA surveillance tRNA decay RNA fragment catabolic process nuclear polyadenylation-dependent rRNA catabolic process rRNA catabolic process regulation of primary metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process nuclear polyadenylation-dependent mRNA catabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality positive regulation of nucleobase-containing compound metabolic process positive regulation of mRNA metabolic process positive regulation of RNA metabolic process polyadenylation-dependent mRNA catabolic process positive regulation of biological process mRNA destabilization regulation of mRNA catabolic process RNA destabilization regulation of catabolic process positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle protein-containing complex TRAMP complex nuclear protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D, G	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, D, G	IPR002121	HRDC domain	Domain
A, D, G	IPR012588	Exosome-associated factor Rrp6, N-terminal	Domain
A, D, G	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, D, G	IPR045092	Exosome complex exonuclease Rrp6-like	Family
A, D, G	IPR002562	3'-5' exonuclease domain	Domain
A, D, G	IPR049559	Rrp6-like, 3'-5' exonuclease domain	Domain
A, D, G	IPR010997	HRDC-like superfamily	Homologous Superfamily
A, D, G	IPR044876	HRDC domain superfamily	Homologous Superfamily
B, E, H	IPR011082	Exosome-associated factor Rrp47/DNA strand repair C1D	Family
B, E, H	IPR007146	Sas10/Utp3/C1D	Family
C, F, I	IPR048392	Exosome RNA helicase MTR4-like, stalk	Domain
C, F, I	IPR012961	ATP-dependent RNA helicase Ski2/MTR4, C-terminal	Domain
C, F, I	IPR025696	Exosome RNA helicase MTR4-like, beta-barrel domain	Domain
C, F, I	IPR016438	ATP-dependent RNA helicase SKI2-like	Family
C, F, I	IPR011545	DEAD/DEAH box helicase domain	Domain
C, F, I	IPR011254	Prismane-like superfamily	Homologous Superfamily
C, F, I	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C, F, I	IPR001650	Helicase, C-terminal domain-like	Domain
C, F, I	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain