2JEB

Structure of a 9-subunit archaeal exosome bound to Mn ions

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2jeba1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	Ribonuclease PH domain 1-like	Exosome complex exonuclease 2,ECX2	(Saccharolobus solfataricus ) [TaxId: 2287 ],	SCOPe (2.08)
A	d2jeba2	Alpha and beta proteins (a+b)	Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	Exosome complex exonuclease 2, ECX2	(Saccharolobus solfataricus ) [TaxId: 2287 ],	SCOPe (2.08)
A	d2jeba3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Saccharolobus solfataricus ) [TaxId: 2287 ],	SCOPe (2.08)
B	d2jebb1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	Ribonuclease PH domain 1-like	Exosome complex exonuclease 1, ECX1	(Saccharolobus solfataricus ) [TaxId: 2287 ],	SCOPe (2.08)
B	d2jebb2	Alpha and beta proteins (a+b)	Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	Exosome complex exonuclease 1, ECX1	(Saccharolobus solfataricus ) [TaxId: 2287 ],	SCOPe (2.08)
C [auth I]	d2jebi2	All beta proteins	OB-fold	Nucleic acid-binding proteins	DNA replication initiator (cdc21/cdc54) N-terminal domain	DNA replication initiator (cdc21/cdc54) N-terminal domain	(Saccharolobus solfataricus ) [TaxId: 2287 ],	SCOPe (2.08)
C [auth I]	d2jebi1	All beta proteins	Barrel-sandwich hybrid	Ribosomal L27 protein-like	automated matches	automated matches	(Saccharolobus solfataricus ) [TaxId: 2287 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8034673	3000100	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease PH domain 2-like	8034675	3000346	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8034677	3000100	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribonuclease PH domain 2-like	8034679	3000346	SCOP2B (2022-06-29)
C [auth I]	SCOP2B Superfamily	Eukaryotic type KH-domain (KH-domain type I)	8034684	3001023	SCOP2B (2022-06-29)
C [auth I]	SCOP2B Superfamily	Ribosomal L27 protein-like	8034683	3000539	SCOP2B (2022-06-29)
C [auth I]	SCOP2B Superfamily	Nucleic acid-binding proteins	8034682	3000135	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	RNase_PH_2	e2jebA2	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: RNase_PH_2	ECOD (1.6)
A	RNase_PH_C_1	e2jebA1	A: a+b two layers	X: Ribonuclease PH domain 2-like	H: Ribonuclease PH domain 2 (From Topology)	T: Ribonuclease PH domain 2	F: RNase_PH_C_1	ECOD (1.6)
B	RNase_PH	e2jebB2	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: RNase_PH	ECOD (1.6)
B	RNase_PH_C_3	e2jebB1	A: a+b two layers	X: Ribonuclease PH domain 2-like	H: Ribonuclease PH domain 2 (From Topology)	T: Ribonuclease PH domain 2	F: RNase_PH_C_3	ECOD (1.6)
C [auth I]	S1_5	e2jebI4	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_5	ECOD (1.6)
C [auth I]	KH_6_2	e2jebI3	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Eukaryotic type KH-domain (KH-domain type I)	F: KH_6_2	ECOD (1.6)
C [auth I]	ECR1_N_2	e2jebI5	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Ribosomal L27 protein	F: ECR1_N_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.230.70	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
B	3.30.230.70	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
C [auth I]	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)
C [auth I]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
C [auth I]	3.30.1370.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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
B	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	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
C [auth I]	PF22625	Exosome RNA binding protein RRP4 N-terminal domain (ECR1_N_2)	Exosome RNA binding protein RRP4 N-terminal domain	This domain is found N-terminal in exosome RNA binding protein RRP4 and related proteins [1-5]. RRP4 is a part of the exosome regulatory substrate recognition platform. This domain is structurally similar to ribosomal L27 protein.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	EXOSOME COMPLEX EXONUCLEASE 2	mRNA 3'-UTR binding RNA binding mRNA 3'-UTR AU-rich region binding binding organic cyclic compound 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 macromolecule metabolic process rRNA metabolic process RNA catabolic process	exosome (RNase complex) protein-containing complex intracellular anatomical structure catalytic complex cytoplasm cellular anatomical entity cytoplasmic exosome (RNase complex) exoribonuclease complex
B	EXOSOME COMPLEX EXONUCLEASE 1	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 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 RNA binding binding organic cyclic compound binding nucleic acid 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 macromolecule metabolic process rRNA metabolic process RNA catabolic process	exosome (RNase complex) protein-containing complex intracellular anatomical structure catalytic complex cytoplasm cellular anatomical entity cytoplasmic exosome (RNase complex) exoribonuclease complex
C [auth I]	EXOSOME COMPLEX RNA-BINDING PROTEIN 1	RNA binding binding organic cyclic compound binding poly(A) binding poly-purine tract binding nucleic acid binding single-stranded RNA binding	nucleobase-containing compound metabolic process CUT metabolic process CUT catabolic process RNA metabolic process metabolic process primary metabolic process macromolecule metabolic process nucleic acid metabolic process sno(s)RNA processing cellular biosynthetic process cellular metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleobase-containing compound metabolic process CUT metabolic process CUT catabolic process RNA metabolic process metabolic process primary metabolic process macromolecule metabolic process nucleic acid metabolic process sno(s)RNA processing cellular biosynthetic process cellular metabolic process 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 cellular process 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 regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of biological process positive regulation of nucleobase-containing compound metabolic process negative regulation of metabolic process positive regulation of mRNA metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process regulation of gene expression negative regulation of gene expression negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process regulation of metabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process positive regulation of biological process mRNA destabilization macromolecule catabolic process regulation of mRNA catabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process RNA destabilization nuclear-transcribed mRNA catabolic process biological regulation regulation of macromolecule metabolic process regulation of catabolic process mRNA metabolic process regulation of cellular biosynthetic process positive regulation of catabolic process regulation of mRNA stability negative regulation of biosynthetic process positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process	intracellular organelle intracellular anatomical structure organelle cellular anatomical entity exosome (RNase complex) protein-containing complex catalytic complex exoribonuclease complex cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR027408	PNPase/RNase PH domain superfamily	Homologous Superfamily
A	IPR001247	Exoribonuclease, phosphorolytic domain 1	Domain
A	IPR050590	Exosome complex component Rrp42 subfamily	Family
A	IPR036345	Exoribonuclease, PH domain 2 superfamily	Homologous Superfamily
A	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
A	IPR015847	Exoribonuclease, phosphorolytic domain 2	Domain
A	IPR020869	Exosome complex component Rrp42, archaea	Family
B	IPR011807	Exosome complex component Rrp41	Family
B	IPR027408	PNPase/RNase PH domain superfamily	Homologous Superfamily
B	IPR001247	Exoribonuclease, phosphorolytic domain 1	Domain
B	IPR036345	Exoribonuclease, PH domain 2 superfamily	Homologous Superfamily
B	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
B	IPR015847	Exoribonuclease, phosphorolytic domain 2	Domain
B	IPR050080	Ribonuclease PH	Family
C [auth I]	IPR054371	Exosome RNA binding protein RRP4, N-terminal domain	Domain
C [auth I]	IPR003029	S1 domain	Domain
C [auth I]	IPR023474	Exosome complex component Rrp4	Family
C [auth I]	IPR048565	RRP4, S1 domain	Domain
C [auth I]	IPR036612	K Homology domain, type 1 superfamily	Homologous Superfamily
C [auth I]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
C [auth I]	IPR026699	Exosome complex RNA-binding protein 1/RRP40/RRP4	Family
C [auth I]	IPR004088	K Homology domain, type 1	Domain