Annotations: 8XIE

Archaeal exosome complex (Rrp4-Rrp41-Rrp42)

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)
D	WD40	e8xieD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
C	WD40	e8xieC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
A		e8xieA01	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F:	ECOD (v294.2)
I [auth H]	WD40	e8xieH1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
H [auth I]	WD40	e8xieI1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
G		e8xieG01	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F:	ECOD (v294.2)
F	WD40	e8xieF1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
E	WD40	e8xieE1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
B		e8xieB01	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F:	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, D	PF03725	3' exoribonuclease family, domain 2 (RNase_PH_C)	3' exoribonuclease family, domain 2	This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of ...	This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components, Swiss:P46948 Swiss:Q12277 and Swiss:P25359 contain a copy of this domain [1]. Swiss:Q10205, a hypothetical protein from S. pombe appears to belong to an uncharacterised subfamily. This subfamily is found in both eukaryotes and archaebacteria.	Domain
A, C, D	PF01138	3' exoribonuclease family, domain 1 (RNase_PH)	3' exoribonuclease family, domain 1	This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of ...	This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components, Swiss:P46948 Swiss:Q12277 and Swiss:P25359 contain a copy of this domain [1]. Swiss:Q10205, a hypothetical protein from S. pombe appears to belong to an uncharacterised subfamily. This subfamily is found in both eukaryotes and archaebacteria.	Domain
G, H [auth I], I [auth H]	PF21266	RRP4, S1 domain (S1_RRP4)	RRP4, S1 domain	Exosome complex component RRP4 is a non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. It consists of a N-terminal beta-sandw ...	Exosome complex component RRP4 is a non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. It consists of a N-terminal beta-sandwich hybrid domain (Pfam:PF14382), a central S1 domain and a C-terminal KH domain (Pfam:PF15985). This entry represents the S1 RNA binding domain, which has an OB fold [1,2].	Domain
G, H [auth I], I [auth H]	PF00013	KH domain (KH_1)	KH domain	KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.	Domain
B, E, F	PF03725	3' exoribonuclease family, domain 2 (RNase_PH_C)	3' exoribonuclease family, domain 2	This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of ...	This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components, Swiss:P46948 Swiss:Q12277 and Swiss:P25359 contain a copy of this domain [1]. Swiss:Q10205, a hypothetical protein from S. pombe appears to belong to an uncharacterised subfamily. This subfamily is found in both eukaryotes and archaebacteria.	Domain
B, E, F	PF01138	3' exoribonuclease family, domain 1 (RNase_PH)	3' exoribonuclease family, domain 1	This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of ...	This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components, Swiss:P46948 Swiss:Q12277 and Swiss:P25359 contain a copy of this domain [1]. Swiss:Q10205, a hypothetical protein from S. pombe appears to belong to an uncharacterised subfamily. This subfamily is found in both eukaryotes and archaebacteria.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, D	Exosome complex component Rrp41	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 RNA binding 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 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 rRNA catabolic process rRNA metabolic process	exosome (RNase complex) protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex cytoplasm cytoplasmic exosome (RNase complex) exoribonuclease complex
G, H [auth I], I [auth H]	Exosome complex component Rrp4	RNA binding binding poly(A) binding poly-purine tract binding nucleic acid binding single-stranded RNA binding	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 CUT catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process sno(s)RNA processing 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 CUT catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process sno(s)RNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process sno(s)RNA 3'-end processing biosynthetic process sno(s)RNA metabolic process RNA 3'-end processing RNA processing poly(A)-dependent snoRNA 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 U4 snRNA 3'-end processing snRNA 3'-end processing snRNA metabolic process snRNA processing	exosome (RNase complex) protein-containing complex intracellular anatomical structure cellular anatomical structure catalytic complex exoribonuclease complex cytoplasm
B, E, F	Exosome complex component Rrp42	mRNA 3'-UTR binding RNA binding mRNA 3'-UTR AU-rich region binding binding nucleic acid binding mRNA binding	catabolic process RNA metabolic process primary metabolic process rRNA catabolic 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 rRNA metabolic process RNA catabolic process	exosome (RNase complex) protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex cytoplasm cytoplasmic exosome (RNase complex) exoribonuclease complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, D	IPR011807	Exosome complex component Rrp41	Family
A, C, D	IPR050080	Ribonuclease PH	Family
A, C, D	IPR027408	PNPase/RNase PH domain superfamily	Homologous Superfamily
A, C, D	IPR001247	Exoribonuclease, phosphorolytic domain 1	Domain
A, C, D	IPR036345	Exoribonuclease, PH domain 2 superfamily	Homologous Superfamily
A, C, D	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
A, C, D	IPR015847	Exoribonuclease, phosphorolytic domain 2	Domain
G, H [auth I], I [auth H]	IPR003029	S1 domain	Domain
G, H [auth I], I [auth H]	IPR023474	Exosome complex component Rrp4	Family
G, H [auth I], I [auth H]	IPR004087	K Homology domain	Domain
G, H [auth I], I [auth H]	IPR048565	RRP4, S1 domain	Domain
G, H [auth I], I [auth H]	IPR036612	K Homology domain, type 1 superfamily	Homologous Superfamily
G, H [auth I], I [auth H]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
G, H [auth I], I [auth H]	IPR026699	Exosome complex RNA-binding protein 1/RRP40/RRP4	Family
G, H [auth I], I [auth H]	IPR004088	K Homology domain, type 1	Domain
B, E, F	IPR027408	PNPase/RNase PH domain superfamily	Homologous Superfamily
B, E, F	IPR001247	Exoribonuclease, phosphorolytic domain 1	Domain
B, E, F	IPR050590	Exosome complex component Rrp42 subfamily	Family
B, E, F	IPR036345	Exoribonuclease, PH domain 2 superfamily	Homologous Superfamily
B, E, F	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
B, E, F	IPR015847	Exoribonuclease, phosphorolytic domain 2	Domain
B, E, F	IPR020869	Exosome complex component Rrp42, archaea	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.

8XIE | pdb_00008xie

Archaeal exosome complex (Rrp4-Rrp41-Rrp42)

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