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Conserved domains on  [gi|17507825|ref|NP_492751|]
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Ribosomal RNA-processing protein 40 [Caenorhabditis elegans]

Protein Classification

exosome complex RNA-binding protein( domain architecture ID 16789758)

exosome complex RNA-binding protein such as exosome complex component RRP40, 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

Gene Ontology:  GO:0003723|GO:0000178
PubMed:  25625331|8696973

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
S1_Rrp40 cd05790
S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 55-140 5.56e-44

S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


:

Pssm-ID: 240216  Cd Length: 86  Bit Score: 142.40  E-value: 5.56e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17507825  55 RYIPQEGDRVIAIVTSKTGDFFRLDIGTAEYAMINFTNFEGATKRNRPNLKTGDIIYATVFDTTPRTEAELTCVDDEKRA 134
Cdd:cd05790   1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANRDMEPELSCVDSSGKA 80


                ....*.
gi 17507825 135 RGMGQL 140
Cdd:cd05790  81 DGFGPL 86
KH-I_Rrp40 cd22526
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp40 and similar ...
 142-210 2.18e-27

type I K homology (KH) RNA-binding domain found in exosome complex component Rrp40 and similar proteins; Rrp40, also called exosome component 3 (EXOSC3), or ribosomal RNA-processing protein 40, 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. Mutations of EXOSC3 gene are associated with neurological diseases. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


:

Pssm-ID: 411954 [Multi-domain]  Cd Length: 78  Bit Score: 99.52  E-value: 2.18e-27
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17507825 142 GGFMFKVSLNHCRRLINPSCKILQTVGKFFKFEITVGMNGRIWISASTSDDIIKIHDIINKSEFITDED 210
Cdd:cd22526   1 GGFLFKVSLGLARRLLSPDCPLLKELGKHFPFEIAVGMNGRIWVKAETVQQTIAIANAIEACEFLSEAQ 69
 
Name Accession Description Interval E-value
S1_Rrp40 cd05790
S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 55-140 5.56e-44

S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 240216  Cd Length: 86  Bit Score: 142.40  E-value: 5.56e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17507825  55 RYIPQEGDRVIAIVTSKTGDFFRLDIGTAEYAMINFTNFEGATKRNRPNLKTGDIIYATVFDTTPRTEAELTCVDDEKRA 134
Cdd:cd05790   1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANRDMEPELSCVDSSGKA 80


                ....*.
gi 17507825 135 RGMGQL 140
Cdd:cd05790  81 DGFGPL 86
KH-I_Rrp40 cd22526
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp40 and similar ...
 142-210 2.18e-27

type I K homology (KH) RNA-binding domain found in exosome complex component Rrp40 and similar proteins; Rrp40, also called exosome component 3 (EXOSC3), or ribosomal RNA-processing protein 40, 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. Mutations of EXOSC3 gene are associated with neurological diseases. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411954 [Multi-domain]  Cd Length: 78  Bit Score: 99.52  E-value: 2.18e-27
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17507825 142 GGFMFKVSLNHCRRLINPSCKILQTVGKFFKFEITVGMNGRIWISASTSDDIIKIHDIINKSEFITDED 210
Cdd:cd22526   1 GGFLFKVSLGLARRLLSPDCPLLKELGKHFPFEIAVGMNGRIWVKAETVQQTIAIANAIEACEFLSEAQ 69
KH_6 pfam15985
KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause ...
 143-189 2.19e-17

KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause para-neoplastic opsoclonus ataxia.


Pssm-ID: 464959 [Multi-domain]  Cd Length: 47  Bit Score: 72.85  E-value: 2.19e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 17507825   143 GFMFKVSLNHCRRLINpsCKILQTVGKFFKFEITVGMNGRIWISAST 189
Cdd:pfam15985   1 GMLVKVSLSLVRRLLK--SHFLHELGKKGPFEIAVGLNGRIWIKSET 45
PRK04163 PRK04163
exosome complex protein Rrp4;
5-186 1.48e-13

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 67.22  E-value: 1.48e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17507825    5 LPGDVINEpsssDSSIIGYGISVRGQTRIATQPGAFHNDDGKVWLNVHSKRYIPQEGDRVIAIVTSKTGDFFRLDIGTAE 84
Cdd:PRK04163  12 VPGDLLAE----GEFKAGRGTYKENGKIYSTVVGLVDIKDDKVRVIPLEGKYIPKVGDLVIGKVTDVTFSGWEVDINSPY 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17507825   85 YAMINFTNF-EGATKRNRPNLKT----GDIIYATVFDTTPRTEAELTCvddekRARGMGQLNGGFMFKVSLNHCRRLINP 159
Cdd:PRK04163  88 KAYLPVSEVlGRPVNVEGTDLRKyldiGDYIIAKVKDVDRTRDVVLTL-----KGKGLGKIEGGTIVEIKPVKVPRVIGK 162

                        170       180
                 ....*....|....*....|....*..
gi 17507825  160 SCKILQTVGKFFKFEITVGMNGRIWIS 186
Cdd:PRK04163 163 KGSMINMLKEETGCDIIVGQNGRIWIK 189
Rrp4 COG1097
Exosome complex RNA-binding protein Rrp4, contains S1 and KH domains [Intracellular ...
 5-186 1.22e-12

Exosome complex RNA-binding protein Rrp4, contains S1 and KH domains [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 440714 [Multi-domain]  Cd Length: 234  Bit Score: 64.87  E-value: 1.22e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17507825   5 LPGDVInepsSSDSSIIGYGISVRGQTRIATQPGAFHNDDGKVWLNVHSKRYIPQEGDRVIAIVTSKTGDFFRLDIGTAE 84
Cdd:COG1097  11 VPGDLL----AEGEYKPGSGTYVEGGKIYSTVLGLVEIKDDKVSVIPLEGKYIPKVGDLVIGKVTDVGPSNWEVDINSPY 86

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17507825  85 YAMINFTN-FEGATKRNRPN----LKTGDIIYATVFDTTPRTEAELTCvddekRARGMGQLNGGFMFKVSLNHCRRLINP 159
Cdd:COG1097  87 QALLPVSEvPGRPFNVESDDlrkyLDIGDYILAKVKNFDRTRDPLLTM-----KDKGLGKIEGGRIVEISPSKVPRVIGK 161

                       170       180
                ....*....|....*....|....*..
gi 17507825 160 SCKILQTVGKFFKFEITVGMNGRIWIS 186
Cdd:COG1097 162 KGSMINMLKKETGCEIIVGQNGRIWIK 188
 
Name Accession Description Interval E-value
S1_Rrp40 cd05790
S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 55-140 5.56e-44

S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 240216  Cd Length: 86  Bit Score: 142.40  E-value: 5.56e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17507825  55 RYIPQEGDRVIAIVTSKTGDFFRLDIGTAEYAMINFTNFEGATKRNRPNLKTGDIIYATVFDTTPRTEAELTCVDDEKRA 134
Cdd:cd05790   1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANRDMEPELSCVDSSGKA 80


                ....*.
gi 17507825 135 RGMGQL 140
Cdd:cd05790  81 DGFGPL 86
KH-I_Rrp40 cd22526
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp40 and similar ...
 142-210 2.18e-27

type I K homology (KH) RNA-binding domain found in exosome complex component Rrp40 and similar proteins; Rrp40, also called exosome component 3 (EXOSC3), or ribosomal RNA-processing protein 40, 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. Mutations of EXOSC3 gene are associated with neurological diseases. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411954 [Multi-domain]  Cd Length: 78  Bit Score: 99.52  E-value: 2.18e-27
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17507825 142 GGFMFKVSLNHCRRLINPSCKILQTVGKFFKFEITVGMNGRIWISASTSDDIIKIHDIINKSEFITDED 210
Cdd:cd22526   1 GGFLFKVSLGLARRLLSPDCPLLKELGKHFPFEIAVGMNGRIWVKAETVQQTIAIANAIEACEFLSEAQ 69
KH_6 pfam15985
KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause ...
 143-189 2.19e-17

KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause para-neoplastic opsoclonus ataxia.


Pssm-ID: 464959 [Multi-domain]  Cd Length: 47  Bit Score: 72.85  E-value: 2.19e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 17507825   143 GFMFKVSLNHCRRLINpsCKILQTVGKFFKFEITVGMNGRIWISAST 189
Cdd:pfam15985   1 GMLVKVSLSLVRRLLK--SHFLHELGKKGPFEIAVGLNGRIWIKSET 45
S1_Rrp4_like cd04454
S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in ...
 55-131 1.53e-16

S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 239901 [Multi-domain]  Cd Length: 82  Bit Score: 71.81  E-value: 1.53e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17507825  55 RYIPQEGDRVIAIVTSKTGDFFRLDIGTAEYAMINFTNFEGA-TKRNRPNLKTGDIIYATVFDTTPRTEAELTCVDDE 131
Cdd:cd04454   1 RYLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKdKKEIRKSLQPGDLILAKVISLGDDMNVLLTTADNE 78
PRK04163 PRK04163
exosome complex protein Rrp4;
5-186 1.48e-13

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 67.22  E-value: 1.48e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17507825    5 LPGDVINEpsssDSSIIGYGISVRGQTRIATQPGAFHNDDGKVWLNVHSKRYIPQEGDRVIAIVTSKTGDFFRLDIGTAE 84
Cdd:PRK04163  12 VPGDLLAE----GEFKAGRGTYKENGKIYSTVVGLVDIKDDKVRVIPLEGKYIPKVGDLVIGKVTDVTFSGWEVDINSPY 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17507825   85 YAMINFTNF-EGATKRNRPNLKT----GDIIYATVFDTTPRTEAELTCvddekRARGMGQLNGGFMFKVSLNHCRRLINP 159
Cdd:PRK04163  88 KAYLPVSEVlGRPVNVEGTDLRKyldiGDYIIAKVKDVDRTRDVVLTL-----KGKGLGKIEGGTIVEIKPVKVPRVIGK 162

                        170       180
                 ....*....|....*....|....*..
gi 17507825  160 SCKILQTVGKFFKFEITVGMNGRIWIS 186
Cdd:PRK04163 163 KGSMINMLKEETGCDIIVGQNGRIWIK 189
Rrp4 COG1097
Exosome complex RNA-binding protein Rrp4, contains S1 and KH domains [Intracellular ...
 5-186 1.22e-12

Exosome complex RNA-binding protein Rrp4, contains S1 and KH domains [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 440714 [Multi-domain]  Cd Length: 234  Bit Score: 64.87  E-value: 1.22e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17507825   5 LPGDVInepsSSDSSIIGYGISVRGQTRIATQPGAFHNDDGKVWLNVHSKRYIPQEGDRVIAIVTSKTGDFFRLDIGTAE 84
Cdd:COG1097  11 VPGDLL----AEGEYKPGSGTYVEGGKIYSTVLGLVEIKDDKVSVIPLEGKYIPKVGDLVIGKVTDVGPSNWEVDINSPY 86

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17507825  85 YAMINFTN-FEGATKRNRPN----LKTGDIIYATVFDTTPRTEAELTCvddekRARGMGQLNGGFMFKVSLNHCRRLINP 159
Cdd:COG1097  87 QALLPVSEvPGRPFNVESDDlrkyLDIGDYILAKVKNFDRTRDPLLTM-----KDKGLGKIEGGRIVEISPSKVPRVIGK 161

                       170       180
                ....*....|....*....|....*..
gi 17507825 160 SCKILQTVGKFFKFEITVGMNGRIWIS 186
Cdd:COG1097 162 KGSMINMLKKETGCEIIVGQNGRIWIK 188
KH-I_Rrp4_Rrp40 cd22445
type I K homology (KH) RNA-binding domain found in exosome complex components Rrp4, Rrp40 and ...
 143-189 4.83e-09

type I K homology (KH) RNA-binding domain found in exosome complex components Rrp4, Rrp40 and similar proteins; The family includes two ribosomal RNA-processing proteins, Rrp4 and Rrp40. They are non-catalytic components of the RNA exosome complex which has 3'-->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. Eukaryotic Rrp4 and Rrp40 contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411873 [Multi-domain]  Cd Length: 78  Bit Score: 51.49  E-value: 4.83e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 17507825 143 GFMFKVSLNHCRRLINPSCKILQTVGKFFKFEITVGMNGRIWISAST 189
Cdd:cd22445   1 GLLVKVTPGLVRRLLAPDCEIIQEVGKLYPLEIVFGMNGRIWVKAKT 47
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 55-140 5.00e-04

S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 240215 [Multi-domain]  Cd Length: 86  Bit Score: 37.91  E-value: 5.00e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17507825  55 RYIPQEGDRVIAIVTSKTGDFFRLDIGTAEYAMINFTNF-EGATKRNRPNLKT----GDIIYATVFDTTPRTEAELTCvd 129
Cdd:cd05789   1 RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVnLPRTDEDELNMRSyldeGDLIVAEVQSVDSDGSVSLHT-- 78

                        90
                ....*....|.
gi 17507825 130 dekRARGMGQL 140
Cdd:cd05789  79 ---RSLKYGKL 86
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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