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Conserved domains on  [gi|145329617|ref|NP_001077958|]
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PNAS-3-like protein [Arabidopsis thaliana]

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 ...
 43-128 9.92e-47

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: 148.95  E-value: 9.92e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329617  43 RYVPRPEDHVLGIVVDCKGENYWIDIKGPQLALLPVLAFEGANRRNYPKFEVSTLLYTRVVKTNTGMNPELSCVDESGKA 122
Cdd:cd05790    1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANRDMEPELSCVDSSGKA 80


                 ....*.
gi 145329617 123 AGFGPL 128
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 ...
 130-208 1.12e-33

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: 115.31  E-value: 1.12e-33
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 145329617 130 DGFMFETSTGLSRMLLSSPtCPVLEALGKKLSFETAFGLNGRCWVHAAAPRIVIIVANALMNSETLSGTQQRIMVEKLL 208
Cdd:cd22526    1 GGFLFKVSLGLARRLLSPD-CPLLKELGKHFPFEIAVGMNGRIWVKAETVQQTIAIANAIEACEFLSEAQIKAMVKKLA 78
 
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 ...
 43-128 9.92e-47

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: 148.95  E-value: 9.92e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329617  43 RYVPRPEDHVLGIVVDCKGENYWIDIKGPQLALLPVLAFEGANRRNYPKFEVSTLLYTRVVKTNTGMNPELSCVDESGKA 122
Cdd:cd05790    1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANRDMEPELSCVDSSGKA 80


                 ....*.
gi 145329617 123 AGFGPL 128
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 ...
 130-208 1.12e-33

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: 115.31  E-value: 1.12e-33
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 145329617 130 DGFMFETSTGLSRMLLSSPtCPVLEALGKKLSFETAFGLNGRCWVHAAAPRIVIIVANALMNSETLSGTQQRIMVEKLL 208
Cdd:cd22526    1 GGFLFKVSLGLARRLLSPD-CPLLKELGKHFPFEIAVGMNGRIWVKAETVQQTIAIANAIEACEFLSEAQIKAMVKKLA 78
KH_6 pfam15985
KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause ...
 131-180 5.57e-12

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: 58.22  E-value: 5.57e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 145329617  131 GFMFETSTGLSRMLLSsptCPVLEALGKKLSFETAFGLNGRCWVHAAAPR 180
Cdd:pfam15985   1 GMLVKVSLSLVRRLLK---SHFLHELGKKGPFEIAVGLNGRIWIKSETVK 47
PRK04163 PRK04163
exosome complex protein Rrp4;
43-189 8.85e-08

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 50.66  E-value: 8.85e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329617  43 RYVPRPEDHVLGIVVDCKGENYWIDIKGPQLALLPV-------LAFEGANRRNYpkFEVSTLLYTRVVKTNTGMNPELSC 115
Cdd:PRK04163  58 KYIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVsevlgrpVNVEGTDLRKY--LDIGDYIIAKVKDVDRTRDVVLTL 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329617 116 VDEsgkaaGFGPLKDGFMFEtstglsrmlLSSPTCP--------VLEALGKKLSFETAFGLNGRCWVHAAAPRIVIIVAN 187
Cdd:PRK04163 136 KGK-----GLGKIEGGTIVE---------IKPVKVPrvigkkgsMINMLKEETGCDIIVGQNGRIWIKGPDEEDEEIAIE 201


                 ..
gi 145329617 188 AL 189
Cdd:PRK04163 202 AI 203
 
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 ...
 43-128 9.92e-47

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: 148.95  E-value: 9.92e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329617  43 RYVPRPEDHVLGIVVDCKGENYWIDIKGPQLALLPVLAFEGANRRNYPKFEVSTLLYTRVVKTNTGMNPELSCVDESGKA 122
Cdd:cd05790    1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANRDMEPELSCVDSSGKA 80


                 ....*.
gi 145329617 123 AGFGPL 128
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 ...
 130-208 1.12e-33

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: 115.31  E-value: 1.12e-33
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 145329617 130 DGFMFETSTGLSRMLLSSPtCPVLEALGKKLSFETAFGLNGRCWVHAAAPRIVIIVANALMNSETLSGTQQRIMVEKLL 208
Cdd:cd22526    1 GGFLFKVSLGLARRLLSPD-CPLLKELGKHFPFEIAVGMNGRIWVKAETVQQTIAIANAIEACEFLSEAQIKAMVKKLA 78
KH_6 pfam15985
KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause ...
 131-180 5.57e-12

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: 58.22  E-value: 5.57e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 145329617  131 GFMFETSTGLSRMLLSsptCPVLEALGKKLSFETAFGLNGRCWVHAAAPR 180
Cdd:pfam15985   1 GMLVKVSLSLVRRLLK---SHFLHELGKKGPFEIAVGLNGRIWIKSETVK 47
S1_Rrp4_like cd04454
S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in ...
 43-117 2.93e-11

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: 57.56  E-value: 2.93e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 145329617  43 RYVPRPEDHVLGIVVDCKGENYWIDIKGPQLALLPVLAFEGA-NRRNYPKFEVSTLLYTRVVKTNTGMNPELSCVD 117
Cdd:cd04454    1 RYLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKdKKEIRKSLQPGDLILAKVISLGDDMNVLLTTAD 76
PRK04163 PRK04163
exosome complex protein Rrp4;
43-189 8.85e-08

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 50.66  E-value: 8.85e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329617  43 RYVPRPEDHVLGIVVDCKGENYWIDIKGPQLALLPV-------LAFEGANRRNYpkFEVSTLLYTRVVKTNTGMNPELSC 115
Cdd:PRK04163  58 KYIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVsevlgrpVNVEGTDLRKY--LDIGDYIIAKVKDVDRTRDVVLTL 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145329617 116 VDEsgkaaGFGPLKDGFMFEtstglsrmlLSSPTCP--------VLEALGKKLSFETAFGLNGRCWVHAAAPRIVIIVAN 187
Cdd:PRK04163 136 KGK-----GLGKIEGGTIVE---------IKPVKVPrvigkkgsMINMLKEETGCDIIVGQNGRIWIKGPDEEDEEIAIE 201


                 ..
gi 145329617 188 AL 189
Cdd:PRK04163 202 AI 203
KH-I_Rrp4_Rrp40 cd22445
type I K homology (KH) RNA-binding domain found in exosome complex components Rrp4, Rrp40 and ...
 131-209 6.33e-06

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: 43.02  E-value: 6.33e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 145329617 131 GFMFETSTGLSRMLLSsPTCPVLEALGKKLSFETAFGLNGRCWVHAAAPRIVIIVANALMNSETLSGTQQRIMVEKLLE 209
Cdd:cd22445    1 GLLVKVTPGLVRRLLA-PDCEIIQEVGKLYPLEIVFGMNGRIWVKAKTRQQTSILANIIEACEHMHTSDQRKQIFSRLA 78
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 43-114 7.95e-06

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: 42.92  E-value: 7.95e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 145329617  43 RYVPRPEDHVLGIVVDCKGENYWIDIKGPQLALLPVLAF-------EGANRRNYpkFEVSTLLYTRVVKTNTGMNPELS 114
Cdd:cd05789    1 RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVnlprtdeDELNMRSY--LDEGDLIVAEVQSVDSDGSVSLH 77
 
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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