4WFD | pdb_00004wfd

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)
E	SCOP2B Superfamily	Rrp6-Rrp47 interacting regions-like	8055987	3002328	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Rrp6-Rrp47 interacting regions-like	8055987	3002328	SCOP2B (2022-06-29)
G	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)
A	SCOP2B Superfamily	Rrp6-Rrp47 interacting regions-like	8055988	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)
H	Peptidase_M99_C	e4wfdH1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Peptidase_M99_C	ECOD (v294.1)
E	Peptidase_M99_C	e4wfdE1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Peptidase_M99_C	ECOD (v294.1)
B	Peptidase_M99_C	e4wfdB1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Peptidase_M99_C	ECOD (v294.1)
G	Peptidase_M99_C	e4wfdG1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Peptidase_M99_C	ECOD (v294.1)
D	Peptidase_M99_C	e4wfdD1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Peptidase_M99_C	ECOD (v294.1)
A	Peptidase_M99_C	e4wfdA1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Peptidase_M99_C	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, E, H	PF04000	Sas10/Utp3/C1D family (Sas10_Utp3)	Sas10/Utp3/C1D family	-	Family
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F, I	ATP-dependent RNA helicase DOB1	oxidoreductase activity catalytic activity nucleic acid conformation isomerase activity isomerase 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 macromolecular conformation isomerase activity binding adenyl ribonucleotide binding oxidoreductase activity catalytic activity nucleic acid conformation isomerase activity isomerase 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 macromolecular conformation isomerase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding RNA binding nucleic acid 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	RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process U5 snRNA 3'-end processing macromolecule biosynthetic process nucleic acid metabolic process snRNA 3'-end processing nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process snRNA metabolic process biosynthetic process snRNA processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process U5 snRNA 3'-end processing macromolecule biosynthetic process nucleic acid metabolic process snRNA 3'-end processing nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process snRNA metabolic process biosynthetic process snRNA processing metabolic process cellular process RNA 3'-end processing macromolecule metabolic process RNA 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 catabolic process negative regulation of biological process macromolecule catabolic process negative regulation of cellular process RNA surveillance RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear RNA surveillance nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process nuclear mRNA surveillance 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 U4 snRNA 3'-end processing mRNA processing nuclear mRNA surveillance of mRNA 3'-end processing RNA fragment catabolic process nuclear polyadenylation-dependent rRNA catabolic process sno(s)RNA processing sno(s)RNA 3'-end processing sno(s)RNA metabolic process poly(A)-dependent snoRNA 3'-end processing 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 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 positive regulation of cellular 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 tRNA metabolic process TRAMP-dependent tRNA surveillance pathway tRNA surveillance tRNA decay	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen protein-containing complex TRAMP complex nuclear protein-containing complex
B, E, H	Exosome complex protein LRP1	DNA binding 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	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 gene expression nucleobase-containing compound biosynthetic process U5 snRNA 3'-end processing macromolecule biosynthetic process snRNA 3'-end processing RNA biosynthetic process nucleic acid biosynthetic process snRNA metabolic process biosynthetic process snRNA processing RNA 3'-end processing RNA processing sno(s)RNA processing sno(s)RNA 3'-end processing sno(s)RNA metabolic process poly(A)-dependent snoRNA 3'-end processing regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process nuclear polyadenylation-dependent CUT catabolic 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 process negative regulation of macromolecule metabolic process mRNA catabolic process nuclear-transcribed mRNA catabolic process negative regulation of metabolic process nuclear mRNA surveillance mRNA metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process U4 snRNA 3'-end processing	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen exosome (RNase complex) protein-containing complex catalytic complex exoribonuclease complex
A, D, G	Exosome complex exonuclease RRP6	binding nucleoside phosphate 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 catalytic activity, acting on a nucleic acid RNA exonuclease activity, producing 5'-phosphomonoesters 3'-5' exonuclease activity RNA exonuclease activity binding nucleoside phosphate 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 catalytic activity, acting on a nucleic acid RNA exonuclease activity, producing 5'-phosphomonoesters 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity 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 nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process sno(s)RNA metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process sno(s)RNA 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 sno(s)RNA metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process sno(s)RNA catabolic process RNA surveillance RNA catabolic process nuclear polyadenylation-dependent snoRNA catabolic process gene expression nucleobase-containing compound biosynthetic process U5 snRNA 3'-end processing macromolecule biosynthetic process snRNA 3'-end processing RNA biosynthetic process nucleic acid biosynthetic process snRNA metabolic process biosynthetic process snRNA processing RNA 3'-end processing RNA processing nuclear polyadenylation-dependent antisense transcript catabolic process antisense RNA transcript catabolic process antisense RNA metabolic process nuclear polyadenylation-dependent CUT catabolic 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 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 nuclear mRNA surveillance 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 regulation of telomere maintenance regulation of cellular component organization telomere organization regulation of primary metabolic process cellular component organization regulation of nucleobase-containing compound metabolic process chromosome organization regulation of chromosome organization DNA metabolic process regulation of organelle organization telomere maintenance organelle organization regulation of DNA metabolic process U4 snRNA 3'-end processing histone mRNA catabolic process histone mRNA metabolic process nuclear polyadenylation-dependent rRNA catabolic process sno(s)RNA processing sno(s)RNA 3'-end processing poly(A)-dependent snoRNA 3'-end processing 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 biological quality 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 positive regulation of cellular 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 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 tRNA metabolic process TRAMP-dependent tRNA surveillance pathway tRNA surveillance tRNA decay	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen exosome (RNase complex) protein-containing complex catalytic complex exoribonuclease complex nuclear protein-containing complex nuclear exosome (RNase complex)

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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	Circadian oscillator component FRH-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	IPR050699	ATP-dependent RNA helicase SUPV3-like	Family
C, F, I	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
B, E, H	IPR011082	Exosome-associated factor Rrp47/DNA strand repair C1D	Family
B, E, H	IPR007146	Sas10/Utp3/C1D	Family
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