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Conserved domains on  [gi|665404113|ref|NP_001285565|]
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ribosomal RNA processing 40, isoform B [Drosophila melanogaster]

Protein Classification

S1_Rrp40 and KH_6 domain-containing protein( domain architecture ID 13375226)

S1_Rrp40 and KH_6 domain-containing protein

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 ...
 63-148 6.85e-45

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: 145.09  E-value: 6.85e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665404113  63 RYIPARGDLILGIVRAKAGDLYRVDIGATDTASISYLAFEAASKKNRPDLIPGDLIYARVLNASADIEPELVCVNSVGKS 142
Cdd:cd05790    1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANRDMEPELSCVDSSGKA 80


                 ....*.
gi 665404113 143 GKLGVL 148
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 ...
 150-226 1.30e-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: 100.29  E-value: 1.30e-27
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 665404113 150 DGFFFKCSLNLGRMLLRENCPVLAALTRELPYEIAVGVNGRIWLKAHSLKETVALANAISALEQSGCAEIDKICGNL 226
Cdd:cd22526    1 GGFLFKVSLGLARRLLSPDCPLLKELGKHFPFEIAVGMNGRIWVKAETVQQTIAIANAIEACEFLSEAQIKAMVKKL 77
Rrp40_N super family cl39658
Exosome complex exonuclease Rrp40 N-terminal domain; This is the N-terminal domain of Rrp40 of ...
 23-63 6.46e-04

Exosome complex exonuclease Rrp40 N-terminal domain; 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.


The actual alignment was detected with superfamily member pfam18311:

Pssm-ID: 436400  Cd Length: 47  Bit Score: 36.47  E-value: 6.46e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 665404113   23 SKRVILGPGLRRL-DDTVVASKAGPLRHKEPGT-FWVDNYQRR 63
Cdd:pfam18311   5 KKPLKLGPGLRHTpPSTIIPTRAGILHTDPKKNaLWIESNSGR 47
 
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 ...
 63-148 6.85e-45

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: 145.09  E-value: 6.85e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665404113  63 RYIPARGDLILGIVRAKAGDLYRVDIGATDTASISYLAFEAASKKNRPDLIPGDLIYARVLNASADIEPELVCVNSVGKS 142
Cdd:cd05790    1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANRDMEPELSCVDSSGKA 80


                 ....*.
gi 665404113 143 GKLGVL 148
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 ...
 150-226 1.30e-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: 100.29  E-value: 1.30e-27
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 665404113 150 DGFFFKCSLNLGRMLLRENCPVLAALTRELPYEIAVGVNGRIWLKAHSLKETVALANAISALEQSGCAEIDKICGNL 226
Cdd:cd22526    1 GGFLFKVSLGLARRLLSPDCPLLKELGKHFPFEIAVGMNGRIWVKAETVQQTIAIANAIEACEFLSEAQIKAMVKKL 77
KH_6 pfam15985
KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause ...
 151-199 2.53e-14

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: 64.77  E-value: 2.53e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 665404113  151 GFFFKCSLNLGRMLLreNCPVLAALTRELPYEIAVGVNGRIWLKAHSLK 199
Cdd:pfam15985   1 GMLVKVSLSLVRRLL--KSHFLHELGKKGPFEIAVGLNGRIWIKSETVK 47
PRK04163 PRK04163
exosome complex protein Rrp4;
7-213 2.35e-09

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 55.67  E-value: 2.35e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665404113   7 IVMPGERIAAIEELAkskrvilGPGLRRLDDTVVASKAGPLRHKEpGTFWVDNYQRRYIPARGDLILGIVRAKAGDLYRV 86
Cdd:PRK04163  10 IVVPGDLLAEGEFKA-------GRGTYKENGKIYSTVVGLVDIKD-DKVRVIPLEGKYIPKVGDLVIGKVTDVTFSGWEV 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665404113  87 DIGATdtasisYLAF----EAASKKNRPD-------LIPGDLIYARVLNASADIEPELvcvnSVgKSGKLGVLTDGFFFK 155
Cdd:PRK04163  82 DINSP------YKAYlpvsEVLGRPVNVEgtdlrkyLDIGDYIIAKVKDVDRTRDVVL----TL-KGKGLGKIEGGTIVE 150

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665404113 156 CSlnlgrmllrencPV------------LAALTRELPYEIAVGVNGRIWLKAHSLKETVALANAISALEQ 213
Cdd:PRK04163 151 IK------------PVkvprvigkkgsmINMLKEETGCDIIVGQNGRIWIKGPDEEDEEIAIEAIKKIER 208
Rrp40_N pfam18311
Exosome complex exonuclease Rrp40 N-terminal domain; This is the N-terminal domain of Rrp40 of ...
 23-63 6.46e-04

Exosome complex exonuclease Rrp40 N-terminal domain; 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.


Pssm-ID: 436400  Cd Length: 47  Bit Score: 36.47  E-value: 6.46e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 665404113   23 SKRVILGPGLRRL-DDTVVASKAGPLRHKEPGT-FWVDNYQRR 63
Cdd:pfam18311   5 KKPLKLGPGLRHTpPSTIIPTRAGILHTDPKKNaLWIESNSGR 47
 
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 ...
 63-148 6.85e-45

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: 145.09  E-value: 6.85e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665404113  63 RYIPARGDLILGIVRAKAGDLYRVDIGATDTASISYLAFEAASKKNRPDLIPGDLIYARVLNASADIEPELVCVNSVGKS 142
Cdd:cd05790    1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANRDMEPELSCVDSSGKA 80


                 ....*.
gi 665404113 143 GKLGVL 148
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 ...
 150-226 1.30e-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: 100.29  E-value: 1.30e-27
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 665404113 150 DGFFFKCSLNLGRMLLRENCPVLAALTRELPYEIAVGVNGRIWLKAHSLKETVALANAISALEQSGCAEIDKICGNL 226
Cdd:cd22526    1 GGFLFKVSLGLARRLLSPDCPLLKELGKHFPFEIAVGMNGRIWVKAETVQQTIAIANAIEACEFLSEAQIKAMVKKL 77
S1_Rrp4_like cd04454
S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in ...
 63-148 9.08e-20

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: 80.29  E-value: 9.08e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665404113  63 RYIPARGDLILGIVRAKAGDLYRVDIGATDTASISYLAF-EAASKKNRPDLIPGDLIYARVLNASADIEPELVCvnsvgK 141
Cdd:cd04454    1 RYLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSAtEKDKKEIRKSLQPGDLILAKVISLGDDMNVLLTT-----A 75


                 ....*..
gi 665404113 142 SGKLGVL 148
Cdd:cd04454   76 DNELGVI 82
KH_6 pfam15985
KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause ...
 151-199 2.53e-14

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: 64.77  E-value: 2.53e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 665404113  151 GFFFKCSLNLGRMLLreNCPVLAALTRELPYEIAVGVNGRIWLKAHSLK 199
Cdd:pfam15985   1 GMLVKVSLSLVRRLL--KSHFLHELGKKGPFEIAVGLNGRIWIKSETVK 47
PRK04163 PRK04163
exosome complex protein Rrp4;
7-213 2.35e-09

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 55.67  E-value: 2.35e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665404113   7 IVMPGERIAAIEELAkskrvilGPGLRRLDDTVVASKAGPLRHKEpGTFWVDNYQRRYIPARGDLILGIVRAKAGDLYRV 86
Cdd:PRK04163  10 IVVPGDLLAEGEFKA-------GRGTYKENGKIYSTVVGLVDIKD-DKVRVIPLEGKYIPKVGDLVIGKVTDVTFSGWEV 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665404113  87 DIGATdtasisYLAF----EAASKKNRPD-------LIPGDLIYARVLNASADIEPELvcvnSVgKSGKLGVLTDGFFFK 155
Cdd:PRK04163  82 DINSP------YKAYlpvsEVLGRPVNVEgtdlrkyLDIGDYIIAKVKDVDRTRDVVL----TL-KGKGLGKIEGGTIVE 150

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665404113 156 CSlnlgrmllrencPV------------LAALTRELPYEIAVGVNGRIWLKAHSLKETVALANAISALEQ 213
Cdd:PRK04163 151 IK------------PVkvprvigkkgsmINMLKEETGCDIIVGQNGRIWIKGPDEEDEEIAIEAIKKIER 208
KH-I_Rrp4_Rrp40 cd22445
type I K homology (KH) RNA-binding domain found in exosome complex components Rrp4, Rrp40 and ...
 151-213 1.99e-08

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: 49.95  E-value: 1.99e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 665404113 151 GFFFKCSLNLGRMLLRENCPVLAALTRELPYEIAVGVNGRIWLKAHSLKETVALANAISALEQ 213
Cdd:cd22445    1 GLLVKVTPGLVRRLLAPDCEIIQEVGKLYPLEIVFGMNGRIWVKAKTRQQTSILANIIEACEH 63
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 63-133 1.18e-05

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: 42.54  E-value: 1.18e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665404113  63 RYIPARGDLILGIVRAKAGDLYRVDIGATdtasisYLAF----EAASKKNRPD-------LIPGDLIYARVLNASADIEP 131
Cdd:cd05789    1 RYIPEVGDVVIGRVTEVGFKRWKVDINSP------YDAVlplsEVNLPRTDEDelnmrsyLDEGDLIVAEVQSVDSDGSV 74


                 ..
gi 665404113 132 EL 133
Cdd:cd05789   75 SL 76
Rrp40_N pfam18311
Exosome complex exonuclease Rrp40 N-terminal domain; This is the N-terminal domain of Rrp40 of ...
 23-63 6.46e-04

Exosome complex exonuclease Rrp40 N-terminal domain; 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.


Pssm-ID: 436400  Cd Length: 47  Bit Score: 36.47  E-value: 6.46e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 665404113   23 SKRVILGPGLRRL-DDTVVASKAGPLRHKEPGT-FWVDNYQRR 63
Cdd:pfam18311   5 KKPLKLGPGLRHTpPSTIIPTRAGILHTDPKKNaLWIESNSGR 47
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 7-48 3.59e-03

Exosome complex exonuclease RRP4 N-terminal region; ECR1_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.


Pssm-ID: 464162 [Multi-domain]  Cd Length: 38  Bit Score: 34.26  E-value: 3.59e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 665404113    7 IVMPGERIAAIEELakskrvILGPGLRRLDDTVVASKAGPLR 48
Cdd:pfam14382   1 IVLPGERLGSDEEY------MPGHGTYVRDGNIYASVAGTVE 36
 
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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