Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
JSCOP2B SuperfamilyNucleic acid-binding proteins8037618 3000135 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyNucleic acid-binding proteins8037616 3000135 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyNucleic acid-binding proteins8037617 3000135 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyNucleic acid-binding proteins8037614 3000135 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyNucleic acid-binding proteins8034656 3000135 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyEukaryotic type KH-domain (KH-domain type I)8034657 3001023 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
APF01138e5jeaA2 A: a+b two layersX: Ribosomal protein S5 domain 2-like (From Topology)H: Ribosomal protein S5 domain 2-like (From Topology)T: Ribosomal protein S5 domain 2-likeF: PF01138ECOD (1.6)
APF03725e5jeaA1 A: a+b two layersX: Ribonuclease PH domain 2-likeH: Ribonuclease PH domain 2 (From Topology)T: Ribonuclease PH domain 2F: PF03725ECOD (1.6)
EF_UNCLASSIFIEDe5jeaE1 A: a+b two layersX: Ribosomal protein S5 domain 2-like (From Topology)H: Ribosomal protein S5 domain 2-like (From Topology)T: Ribosomal protein S5 domain 2-likeF: F_UNCLASSIFIEDECOD (1.6)
EF_UNCLASSIFIEDe5jeaE2 A: a+b two layersX: Ribonuclease PH domain 2-likeH: Ribonuclease PH domain 2 (From Topology)T: Ribonuclease PH domain 2F: F_UNCLASSIFIEDECOD (1.6)
JPF17215e5jeaJ5 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF17215ECOD (1.6)
JPF17216e5jeaJ3 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF17216ECOD (1.6)
JPF17849e5jeaJ4 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF17849ECOD (1.6)
JPF00773e5jeaJ2 A: beta barrelsX: OB-foldH: RNB domain-like (From Topology)T: RNB domain-likeF: PF00773ECOD (1.6)
JPF13638e5jeaJ1 A: a/b three-layered sandwichesX: HAD domain-likeH: HAD domain-relatedT: PIN domain-likeF: PF13638ECOD (1.6)
KPF00959e5jeaK1 A: a+b complex topologyX: Lysozyme-like (From Homology)H: Lysozyme-likeT: Lysozyme-likeF: PF00959ECOD (1.6)
BPF01138e5jeaB1 A: a+b two layersX: Ribosomal protein S5 domain 2-like (From Topology)H: Ribosomal protein S5 domain 2-like (From Topology)T: Ribosomal protein S5 domain 2-likeF: PF01138ECOD (1.6)
BPF03725e5jeaB2 A: a+b two layersX: Ribonuclease PH domain 2-likeH: Ribonuclease PH domain 2 (From Topology)T: Ribonuclease PH domain 2F: PF03725ECOD (1.6)
CPF01138e5jeaC2 A: a+b two layersX: Ribosomal protein S5 domain 2-like (From Topology)H: Ribosomal protein S5 domain 2-like (From Topology)T: Ribosomal protein S5 domain 2-likeF: PF01138ECOD (1.6)
CF_UNCLASSIFIEDe5jeaC1 A: a+b two layersX: Ribonuclease PH domain 2-likeH: Ribonuclease PH domain 2 (From Topology)T: Ribonuclease PH domain 2F: F_UNCLASSIFIEDECOD (1.6)
DPF01138e5jeaD1 A: a+b two layersX: Ribosomal protein S5 domain 2-like (From Topology)H: Ribosomal protein S5 domain 2-like (From Topology)T: Ribosomal protein S5 domain 2-likeF: PF01138ECOD (1.6)
DPF03725e5jeaD2 A: a+b two layersX: Ribonuclease PH domain 2-likeH: Ribonuclease PH domain 2 (From Topology)T: Ribonuclease PH domain 2F: PF03725ECOD (1.6)
FPF01138e5jeaF2 A: a+b two layersX: Ribosomal protein S5 domain 2-like (From Topology)H: Ribosomal protein S5 domain 2-like (From Topology)T: Ribosomal protein S5 domain 2-likeF: PF01138ECOD (1.6)
FF_UNCLASSIFIEDe5jeaF1 A: a+b two layersX: Ribonuclease PH domain 2-likeH: Ribonuclease PH domain 2 (From Topology)T: Ribonuclease PH domain 2F: F_UNCLASSIFIEDECOD (1.6)
GPF21262e5jeaG3 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF21262ECOD (1.6)
GPF15985e5jeaG1 A: a+b two layersX: Alpha-lytic protease prodomain-likeH: KH-domainsT: Eukaryotic type KH-domain (KH-domain type I)F: PF15985ECOD (1.6)
GPF18311e5jeaG2 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Ribosomal L27 proteinF: PF18311ECOD (1.6)
HPF21266e5jeaH3 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF21266ECOD (1.6)
HPF15985e5jeaH2 A: a+b two layersX: Alpha-lytic protease prodomain-likeH: KH-domainsT: Eukaryotic type KH-domain (KH-domain type I)F: PF15985ECOD (1.6)
HPF14382e5jeaH1 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Ribosomal L27 proteinF: PF14382ECOD (1.6)
IPF10447e5jeaI1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF10447ECOD (1.6)
IPF21551e5jeaI2 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Ribosomal L27 proteinF: PF21551ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF037253' exoribonuclease family, domain 2 (RNase_PH_C)3' exoribonuclease family, domain 2This 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
PF011383' exoribonuclease family, domain 1 (RNase_PH)3' exoribonuclease family, domain 1This 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
PF13638PIN domain (PIN_4)PIN domainMembers of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases).Domain
PF17849Dis3-like cold-shock domain 2 (CSD2) (OB_Dis3)Dis3-like cold-shock domain 2 (CSD2)This domain has an OB fold and is found in the Dis3l2 protein [1]. This domain along with CSD1 binds to RNA.Domain
PF17215S1 domain (Rrp44_S1)S1 domainThis domain corresponds to the S1 domain found at the C-terminus of ribonucleases such as yeast Rrp44 [1].Domain
PF17216Rrp44-like cold shock domain (Rrp44_CSD1)Rrp44-like cold shock domain- Domain
PF00773RNB domain (RNB)RNB domainThis domain is the catalytic domain of ribonuclease II [1].Domain
PF037253' exoribonuclease family, domain 2 (RNase_PH_C)3' exoribonuclease family, domain 2This 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
PF011383' exoribonuclease family, domain 1 (RNase_PH)3' exoribonuclease family, domain 1This 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
PF011383' exoribonuclease family, domain 1 (RNase_PH)3' exoribonuclease family, domain 1This 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
PF037253' exoribonuclease family, domain 2 (RNase_PH_C)3' exoribonuclease family, domain 2This 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
PF011383' exoribonuclease family, domain 1 (RNase_PH)3' exoribonuclease family, domain 1This 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
PF18311Exosome complex exonuclease Rrp40 N-terminal domain (Rrp40_N)Exosome complex exonuclease Rrp40 N-terminal domainThis is the N-terminal domain of Rrp40 of the exosome complex present in Saccharomyces cerevisiae. The RNA exosome complex is responsible for degrading RNA molecules in the 3' to 5' direction. Rrp40 is a 'cap' protein and binds the RNase PH barrel on ...This is the N-terminal domain of Rrp40 of the exosome complex present in Saccharomyces cerevisiae. The RNA exosome complex is responsible for degrading RNA molecules in the 3' to 5' direction. Rrp40 is a 'cap' protein and binds the RNase PH barrel on the opposite side from the S1/KH ring. The N-terminal domain of Rrp44 forms a long beta-hairpin that is wedged in between Rrp41-Rrp42 and approaches the N terminus of the cap protein Rrp4 [1]. This domain adopts a beta- sandwich hybrid structure.
Domain
PF21262Exosome complex component RRP40, S1 domain (RRP40_S1)Exosome complex component RRP40, S1 domainRRP40 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:P ...RRP40 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:PF21261), 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 [1-3].
Domain
PF15985KH domain (KH_6)KH domainKH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause para-neoplastic opsoclonus ataxia.Domain
PF21266RRP4, S1 domain (RRP4_S1)RRP4, S1 domainExosome 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
PF14382Exosome complex exonuclease RRP4 N-terminal region (ECR1_N)Exosome complex exonuclease RRP4 N-terminal regionECR1_N is an N-terminal region of the exosome complex exonuclease RRP proteins. It is a G-rich domain which structurally is a rudimentary single hybrid fold with a permuted topology.Domain
PF15985KH domain (KH_6)KH domainKH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause para-neoplastic opsoclonus ataxia.Domain
PF21551Exosome complex component CSL4, N-terminal domain (CSL4_N)Exosome complex component CSL4, N-terminal domainThis domain is found at the N-terminal end of Exosome complex component CSL4 from Saccharomyces cerevisiae, a non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA ...This domain is found at the N-terminal end of Exosome complex component CSL4 from Saccharomyces cerevisiae, 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 [1-4].
Domain
PF10447Exosome component EXOSC1/CSL4 (EXOSC1)Exosome component EXOSC1/CSL4This family of proteins are components of the exosome 3'->5' exoribonuclease complex. The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions [1].Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Exosome complex component RRP45
Exosome complex component RRP42
Exosome complex exonuclease DIS3
Superkiller protein 7,Endolysin
L [auth R]RNA (29-MER)---
Exosome complex component SKI6
Exosome complex component RRP43
Exosome complex component RRP46
Exosome complex component MTR3
Exosome complex component RRP40
Exosome complex component RRP4
Exosome complex component CSL4

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR033100Exosome complex component RRP45Family
IPR027408PNPase/RNase PH domain superfamilyHomologous Superfamily
IPR001247Exoribonuclease, phosphorolytic domain 1Domain
IPR036345Exoribonuclease, PH domain 2 superfamilyHomologous Superfamily
IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
IPR015847Exoribonuclease, phosphorolytic domain 2Domain
IPR027408PNPase/RNase PH domain superfamilyHomologous Superfamily
IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
IPR041505Dis3-like cold-shock domain 2Domain
IPR003029S1 domainDomain
IPR022966Ribonuclease II/R, conserved siteConserved Site
IPR033770Exosome complex exonuclease RRP44, S1 domainDomain
IPR033771Rrp44-like cold shock domainDomain
IPR002716PIN domainDomain
IPR001900Ribonuclease II/RDomain
IPR029060PIN-like domain superfamilyHomologous Superfamily
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR000795Translational (tr)-type GTP-binding domainDomain
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
IPR001165T4-type lysozymeFamily
IPR034690Endolysin T4 typeFamily
IPR002196Glycoside hydrolase, family 24Family
IPR023347Lysozyme domain superfamilyHomologous Superfamily
IPR023346Lysozyme-like domain superfamilyHomologous Superfamily
IPR027408PNPase/RNase PH domain superfamilyHomologous Superfamily
IPR001247Exoribonuclease, phosphorolytic domain 1Domain
IPR036345Exoribonuclease, PH domain 2 superfamilyHomologous Superfamily
IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
IPR015847Exoribonuclease, phosphorolytic domain 2Domain
IPR027408PNPase/RNase PH domain superfamilyHomologous Superfamily
IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
IPR001247Exoribonuclease, phosphorolytic domain 1Domain
IPR027408PNPase/RNase PH domain superfamilyHomologous Superfamily
IPR001247Exoribonuclease, phosphorolytic domain 1Domain
IPR036345Exoribonuclease, PH domain 2 superfamilyHomologous Superfamily
IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
IPR015847Exoribonuclease, phosphorolytic domain 2Domain
IPR027408PNPase/RNase PH domain superfamilyHomologous Superfamily
IPR001247Exoribonuclease, phosphorolytic domain 1Domain
IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
IPR041054Exosome complex exonuclease Rrp40, N-terminal domain, eukaryotesDomain
IPR037319Rrp40, S1 domainDomain
IPR036612K Homology domain, type 1 superfamilyHomologous Superfamily
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR026699Exosome complex RNA-binding protein 1/RRP40/RRP4Family
IPR004088K Homology domain, type 1Domain
IPR048565RRP4, S1 domainDomain
IPR036612K Homology domain, type 1 superfamilyHomologous Superfamily
IPR025721Exosome complex component, N-terminal domainDomain
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR026699Exosome complex RNA-binding protein 1/RRP40/RRP4Family
IPR004088K Homology domain, type 1Domain
IPR019495Exosome complex component CSL4, C-terminalDomain
IPR039771Exosome complex component Csl4Family
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR048626Exosome complex component CSL4, N-terminal domainDomain