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Conserved domains on  [gi|15218790|ref|NP_171835|]
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ribosomal RNA processing 4 [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KH-I_Rrp4_eukar cd22525
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from ...
 182-313 9.11e-41

type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from eukaryote; The subfamily corresponds to ribosomal RNA-processing protein 4 (Rrp4) mainly from eukaryote. Rrp4, also called exosome component 2 (EXOSC2), or ribosomal RNA-processing protein 4, 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 in EXOSC2 gene are associated with a novel syndrome characterized by retinitis pigmentosa, progressive hearing loss, premature aging, short stature, mild intellectual disability and distinctive gestalt. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


:

Pssm-ID: 411953  Cd Length: 123  Bit Score: 138.56  E-value: 9.11e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15218790 182 GQLLKVDPYLVKRSKHHFHYVESlGIDLIIGCNGFIWVGEHVEVRDpmaiddqkDEEMISSSSTGKEQSHIPLETRQTIC 261
Cdd:cd22525   1 GILVKVPPSLIKRQKSHFHNLPC-GVDVILGLNGYIWISPTVEESG--------EEAGGSAAIYSNNNEPVSPETREAIA 71

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 15218790 262 RIGNAIRVLSNLGFTVTLEVIMETVNLSNSKNIDIHDMLGSEFHVVVAENEA 313
Cdd:cd22525  72 RVRNCIKALAALHIPITDTSILAVYEASLELGIEVKDLLKPEVMEEIVEEAR 123
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 88-179 1.49e-35

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: 123.81  E-value: 1.49e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15218790  88 RYKPEVGDIVVGRVIEVAQKRWRVELNFNQDGVLMLSSMNMPdgiqrrRTSVDELNMRNIFVEHDVVCAEVRNFQHDGSL 167
Cdd:cd05789   1 RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLP------RTDEDELNMRSYLDEGDLIVAEVQSVDSDGSV 74

                        90
                ....*....|..
gi 15218790 168 QLQARSQKYGKL 179
Cdd:cd05789  75 SLHTRSLKYGKL 86
PRK09521 super family cl35849
exosome complex RNA-binding protein Csl4; Provisional
 52-113 6.98e-06

exosome complex RNA-binding protein Csl4; Provisional


The actual alignment was detected with superfamily member PRK09521:

Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 45.74  E-value: 6.98e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15218790   52 FLKGHGTSEVDGELLATVCGVVERVD--KLVYVRTLRAR-YKPEVGDIVVGRVIEVAQKRWRVEL 113
Cdd:PRK09521  20 YLPGEGTYEDNGEVYASVVGKVFIDDinRKISVIPFKKTpPLLKKGDIVYGRVVDVKEQRALVRI 84
 
Name Accession Description Interval E-value
KH-I_Rrp4_eukar cd22525
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from ...
 182-313 9.11e-41

type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from eukaryote; The subfamily corresponds to ribosomal RNA-processing protein 4 (Rrp4) mainly from eukaryote. Rrp4, also called exosome component 2 (EXOSC2), or ribosomal RNA-processing protein 4, 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 in EXOSC2 gene are associated with a novel syndrome characterized by retinitis pigmentosa, progressive hearing loss, premature aging, short stature, mild intellectual disability and distinctive gestalt. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411953  Cd Length: 123  Bit Score: 138.56  E-value: 9.11e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15218790 182 GQLLKVDPYLVKRSKHHFHYVESlGIDLIIGCNGFIWVGEHVEVRDpmaiddqkDEEMISSSSTGKEQSHIPLETRQTIC 261
Cdd:cd22525   1 GILVKVPPSLIKRQKSHFHNLPC-GVDVILGLNGYIWISPTVEESG--------EEAGGSAAIYSNNNEPVSPETREAIA 71

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 15218790 262 RIGNAIRVLSNLGFTVTLEVIMETVNLSNSKNIDIHDMLGSEFHVVVAENEA 313
Cdd:cd22525  72 RVRNCIKALAALHIPITDTSILAVYEASLELGIEVKDLLKPEVMEEIVEEAR 123
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 88-179 1.49e-35

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: 123.81  E-value: 1.49e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15218790  88 RYKPEVGDIVVGRVIEVAQKRWRVELNFNQDGVLMLSSMNMPdgiqrrRTSVDELNMRNIFVEHDVVCAEVRNFQHDGSL 167
Cdd:cd05789   1 RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLP------RTDEDELNMRSYLDEGDLIVAEVQSVDSDGSV 74

                        90
                ....*....|..
gi 15218790 168 QLQARSQKYGKL 179
Cdd:cd05789  75 SLHTRSLKYGKL 86
PRK04163 PRK04163
exosome complex protein Rrp4;
49-219 2.02e-17

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 79.93  E-value: 2.02e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15218790   49 DDAFLKGHGTSEVDGELLATVCGVVERVDKLVYVRTLRARYKPEVGDIVVGRVIEVAQKRWRVELNFNQDGVLMLSSmnm 128
Cdd:PRK04163  19 EGEFKAGRGTYKENGKIYSTVVGLVDIKDDKVRVIPLEGKYIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSE--- 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15218790  129 pdgIQRRRTSVDELNMRNIFVEHDVVCAEVRNFQHDGSLQLQARSQKYGKLEKGQLLKVDPYLVKRskhhfhyV------ 202
Cdd:PRK04163  96 ---VLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGKGLGKIEGGTIVEIKPVKVPR-------Vigkkgs 165

                        170       180
                 ....*....|....*....|...
gi 15218790  203 ------ESLGIDLIIGCNGFIWV 219
Cdd:PRK04163 166 minmlkEETGCDIIVGQNGRIWI 188
KH_6 pfam15985
KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause ...
 182-224 1.65e-07

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: 47.05  E-value: 1.65e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 15218790   182 GQLLKVDPYLVKRSKHHfHYVESLG----IDLIIGCNGFIWVGEHVE 224
Cdd:pfam15985   1 GMLVKVSLSLVRRLLKS-HFLHELGkkgpFEIAVGLNGRIWIKSETV 46
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 52-113 6.98e-06

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 45.74  E-value: 6.98e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15218790   52 FLKGHGTSEVDGELLATVCGVVERVD--KLVYVRTLRAR-YKPEVGDIVVGRVIEVAQKRWRVEL 113
Cdd:PRK09521  20 YLPGEGTYEDNGEVYASVVGKVFIDDinRKISVIPFKKTpPLLKKGDIVYGRVVDVKEQRALVRI 84
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
92-164 3.55e-04

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 38.35  E-value: 3.55e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15218790     92 EVGDIVVGRVIEVAQKRWRVELNFNQDGVLMLSSMNmpdgiqrrrtSVDELNMRNIFVEHDVVCAEVRNFQHD 164
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELS----------DKRVKDPEEVLKVGDEVKVKVLSVDEE 63
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 49-76 1.16e-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: 36.18  E-value: 1.16e-03
                          10        20
                  ....*....|....*....|....*...
gi 15218790    49 DDAFLKGHGTSEVDGELLATVCGVVERV 76
Cdd:pfam14382  11 DEEYMPGHGTYVRDGNIYASVAGTVEIV 38
 
Name Accession Description Interval E-value
KH-I_Rrp4_eukar cd22525
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from ...
 182-313 9.11e-41

type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from eukaryote; The subfamily corresponds to ribosomal RNA-processing protein 4 (Rrp4) mainly from eukaryote. Rrp4, also called exosome component 2 (EXOSC2), or ribosomal RNA-processing protein 4, 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 in EXOSC2 gene are associated with a novel syndrome characterized by retinitis pigmentosa, progressive hearing loss, premature aging, short stature, mild intellectual disability and distinctive gestalt. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411953  Cd Length: 123  Bit Score: 138.56  E-value: 9.11e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15218790 182 GQLLKVDPYLVKRSKHHFHYVESlGIDLIIGCNGFIWVGEHVEVRDpmaiddqkDEEMISSSSTGKEQSHIPLETRQTIC 261
Cdd:cd22525   1 GILVKVPPSLIKRQKSHFHNLPC-GVDVILGLNGYIWISPTVEESG--------EEAGGSAAIYSNNNEPVSPETREAIA 71

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 15218790 262 RIGNAIRVLSNLGFTVTLEVIMETVNLSNSKNIDIHDMLGSEFHVVVAENEA 313
Cdd:cd22525  72 RVRNCIKALAALHIPITDTSILAVYEASLELGIEVKDLLKPEVMEEIVEEAR 123
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 88-179 1.49e-35

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: 123.81  E-value: 1.49e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15218790  88 RYKPEVGDIVVGRVIEVAQKRWRVELNFNQDGVLMLSSMNMPdgiqrrRTSVDELNMRNIFVEHDVVCAEVRNFQHDGSL 167
Cdd:cd05789   1 RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLP------RTDEDELNMRSYLDEGDLIVAEVQSVDSDGSV 74

                        90
                ....*....|..
gi 15218790 168 QLQARSQKYGKL 179
Cdd:cd05789  75 SLHTRSLKYGKL 86
PRK04163 PRK04163
exosome complex protein Rrp4;
49-219 2.02e-17

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 79.93  E-value: 2.02e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15218790   49 DDAFLKGHGTSEVDGELLATVCGVVERVDKLVYVRTLRARYKPEVGDIVVGRVIEVAQKRWRVELNFNQDGVLMLSSmnm 128
Cdd:PRK04163  19 EGEFKAGRGTYKENGKIYSTVVGLVDIKDDKVRVIPLEGKYIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSE--- 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15218790  129 pdgIQRRRTSVDELNMRNIFVEHDVVCAEVRNFQHDGSLQLQARSQKYGKLEKGQLLKVDPYLVKRskhhfhyV------ 202
Cdd:PRK04163  96 ---VLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGKGLGKIEGGTIVEIKPVKVPR-------Vigkkgs 165

                        170       180
                 ....*....|....*....|...
gi 15218790  203 ------ESLGIDLIIGCNGFIWV 219
Cdd:PRK04163 166 minmlkEETGCDIIVGQNGRIWI 188
S1_Rrp4_like cd04454
S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in ...
 88-179 2.58e-15

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: 69.89  E-value: 2.58e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15218790  88 RYKPEVGDIVVGRVIEVAQKRWRVELNFNQDGVLMLSSMNMPdgiqrrrtsvDELNMRNIFVEHDVVCAEVRNFQHDGSL 167
Cdd:cd04454   1 RYLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEK----------DKKEIRKSLQPGDLILAKVISLGDDMNV 70

                        90
                ....*....|..
gi 15218790 168 QLQARSQKYGKL 179
Cdd:cd04454  71 LLTTADNELGVI 82
KH_6 pfam15985
KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause ...
 182-224 1.65e-07

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: 47.05  E-value: 1.65e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 15218790   182 GQLLKVDPYLVKRSKHHfHYVESLG----IDLIIGCNGFIWVGEHVE 224
Cdd:pfam15985   1 GMLVKVSLSLVRRLLKS-HFLHELGkkgpFEIAVGLNGRIWIKSETV 46
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 52-113 6.98e-06

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 45.74  E-value: 6.98e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15218790   52 FLKGHGTSEVDGELLATVCGVVERVD--KLVYVRTLRAR-YKPEVGDIVVGRVIEVAQKRWRVEL 113
Cdd:PRK09521  20 YLPGEGTYEDNGEVYASVVGKVFIDDinRKISVIPFKKTpPLLKKGDIVYGRVVDVKEQRALVRI 84
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
92-164 3.55e-04

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 38.35  E-value: 3.55e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15218790     92 EVGDIVVGRVIEVAQKRWRVELNFNQDGVLMLSSMNmpdgiqrrrtSVDELNMRNIFVEHDVVCAEVRNFQHD 164
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELS----------DKRVKDPEEVLKVGDEVKVKVLSVDEE 63
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 49-76 1.16e-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: 36.18  E-value: 1.16e-03
                          10        20
                  ....*....|....*....|....*...
gi 15218790    49 DDAFLKGHGTSEVDGELLATVCGVVERV 76
Cdd:pfam14382  11 DEEYMPGHGTYVRDGNIYASVAGTVEIV 38
 
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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