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Conserved domains on  [gi|1407938535|pdb|6D6R|I]
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Chain I, Exosome complex component CSL4

Protein Classification

ECR1_N and S1_CSL4 domain-containing protein( domain architecture ID 10627461)

ECR1_N and S1_CSL4 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
S1_CSL4 cd05791
S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 64-156 5.72e-56

S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 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 S. 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: 240217  Cd Length: 92  Bit Score: 172.05  E-value: 5.72e-56
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6R_I       64 QLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSn 143
Cdd:cd05791   1 LVLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASS- 79

                        90
                ....*....|...
6D6R_I      144 YLLTTAENELGVV 156
Cdd:cd05791  80 YYLSTAENELGVV 92
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 10-45 1.42e-08

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: 48.90  E-value: 1.42e-08
                          10        20        30
                  ....*....|....*....|....*....|....*.
6D6R_I         10 CIPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMK 45
Cdd:pfam14382   2 VLPGERLGSDEEYMPGHGTYVRDGNIYASVAGTVEI 37
 
Name Accession Description Interval E-value
S1_CSL4 cd05791
S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 64-156 5.72e-56

S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 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 S. 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: 240217  Cd Length: 92  Bit Score: 172.05  E-value: 5.72e-56
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6R_I       64 QLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSn 143
Cdd:cd05791   1 LVLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASS- 79

                        90
                ....*....|...
6D6R_I      144 YLLTTAENELGVV 156
Cdd:cd05791  80 YYLSTAENELGVV 92
Csl4 COG1096
Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...
 11-188 6.51e-28

Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 440713 [Multi-domain]  Cd Length: 191  Bit Score: 103.44  E-value: 6.51e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6R_I       11 IPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKSSENGalpVVSVVRETESQLLPDVGAIVTCKVSSINSRFAKVHIL 90
Cdd:COG1096  10 LPGDVLAVIEEFLPGEGTYEEDGKIRAAVVGKVVIDDKNR---VISVKPKKKPPPVPKKGDIVIGEVVDVRESMALVKIY 86

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6R_I       91 YVGSM--PLKNSFRGTIRKEDVRATEKDKveIYKSFRPGDIVLAKVISLGdaqSNYLLTTAENELGVVVAH-SESGIQMV 167
Cdd:COG1096  87 AIEGNerELPSSFSGIIHISQVSDSYVKD--LSDEFRVGDIVRAKVISTL---PPIQLSIKEPDLGVIKAKcSKCGSPLV 161

                       170       180
                ....*....|....*....|.
6D6R_I      168 PISwCEMQCPKTHTKEFRKVA 188
Cdd:COG1096 162 KDG-DKLKCPNCGNVEKRKLS 181
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 12-188 7.00e-19

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 80.02  E-value: 7.00e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6R_I        12 PGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKSSENgalPVVSVVRETESQLLPDVGAIVTCKVSSINSRFAKVHILY 91
Cdd:PRK09521  10 PGDYLAVIEEYLPGEGTYEDNGEVYASVVGKVFIDDIN---RKISVIPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVS 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6R_I        92 V--GSMPLKNSFRGTIRKEDVRatEKDKVEIYKSFRPGDIVLAKVISLGDaqsNYLLTTAENELGVVVAH-SESGIQMVP 168
Cdd:PRK09521  87 IegSERELATSKLAYIHISQVS--DGYVESLTDAFKIGDIVRAKVISYTD---PLQLSTKGKDLGVIYAMcSRCRTPLVK 161

                        170       180
                 ....*....|....*....|
6D6R_I       169 ISWCEMQCPKTHTKEFRKVA 188
Cdd:PRK09521 162 KGENELKCPNCGNIETRKLS 181
EXOSC1 pfam10447
Exosome component EXOSC1/CSL4; This family of proteins are components of the exosome 3'->5' ...
 66-137 3.75e-13

Exosome component EXOSC1/CSL4; This 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.


Pssm-ID: 402191  Cd Length: 112  Bit Score: 62.90  E-value: 3.75e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6R_I         66 LPDVGAIVTCKVSSINSRFAKVHIL--------------------YVGSMP--------------------LKNSFRGTI 105
Cdd:pfam10447   1 LPKEGDVVLARVTRLSQQQANVEILsvegennvlgdsgvgsngegAVASIPagggldilfsvstvasqssdLGETFKGII 80

                          90       100       110
                  ....*....|....*....|....*....|..
6D6R_I        106 RKEDVRATEKDKVEIYKSFRPGDIVLAKVISL 137
Cdd:pfam10447  81 RSQDVRATERDRVKVIEMFRPGDIVRAQVISL 112
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 10-45 1.42e-08

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: 48.90  E-value: 1.42e-08
                          10        20        30
                  ....*....|....*....|....*....|....*.
6D6R_I         10 CIPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMK 45
Cdd:pfam14382   2 VLPGERLGSDEEYMPGHGTYVRDGNIYASVAGTVEI 37
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
69-148 4.77e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 39.89  E-value: 4.77e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6R_I          69 VGAIVTCKVSSINSRFAKVHILyvgsmplkNSFRGTIRKEDVraTEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYLLTT 148
Cdd:smart00316   2 VGDVVEGTVTEITPGGAFVDLG--------NGVEGLIPISEL--SDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
 
Name Accession Description Interval E-value
S1_CSL4 cd05791
S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 64-156 5.72e-56

S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 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 S. 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: 240217  Cd Length: 92  Bit Score: 172.05  E-value: 5.72e-56
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6R_I       64 QLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSn 143
Cdd:cd05791   1 LVLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASS- 79

                        90
                ....*....|...
6D6R_I      144 YLLTTAENELGVV 156
Cdd:cd05791  80 YYLSTAENELGVV 92
S1_Rrp4_like cd04454
S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in ...
 64-156 1.60e-32

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: 112.26  E-value: 1.60e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6R_I       64 QLLPDVGAIVTCKVSSINSRFAKVHILYvgsmplknsfRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAqSN 143
Cdd:cd04454   1 RYLPDVGDIVIGIVTEVNSRFWKVDILS----------RGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MN 69

                        90
                ....*....|...
6D6R_I      144 YLLTTAENELGVV 156
Cdd:cd04454  70 VLLTTADNELGVI 82
Csl4 COG1096
Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...
 11-188 6.51e-28

Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 440713 [Multi-domain]  Cd Length: 191  Bit Score: 103.44  E-value: 6.51e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6R_I       11 IPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKSSENGalpVVSVVRETESQLLPDVGAIVTCKVSSINSRFAKVHIL 90
Cdd:COG1096  10 LPGDVLAVIEEFLPGEGTYEEDGKIRAAVVGKVVIDDKNR---VISVKPKKKPPPVPKKGDIVIGEVVDVRESMALVKIY 86

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6R_I       91 YVGSM--PLKNSFRGTIRKEDVRATEKDKveIYKSFRPGDIVLAKVISLGdaqSNYLLTTAENELGVVVAH-SESGIQMV 167
Cdd:COG1096  87 AIEGNerELPSSFSGIIHISQVSDSYVKD--LSDEFRVGDIVRAKVISTL---PPIQLSIKEPDLGVIKAKcSKCGSPLV 161

                       170       180
                ....*....|....*....|.
6D6R_I      168 PISwCEMQCPKTHTKEFRKVA 188
Cdd:COG1096 162 KDG-DKLKCPNCGNVEKRKLS 181
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 12-188 7.00e-19

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 80.02  E-value: 7.00e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6R_I        12 PGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKSSENgalPVVSVVRETESQLLPDVGAIVTCKVSSINSRFAKVHILY 91
Cdd:PRK09521  10 PGDYLAVIEEYLPGEGTYEDNGEVYASVVGKVFIDDIN---RKISVIPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVS 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6R_I        92 V--GSMPLKNSFRGTIRKEDVRatEKDKVEIYKSFRPGDIVLAKVISLGDaqsNYLLTTAENELGVVVAH-SESGIQMVP 168
Cdd:PRK09521  87 IegSERELATSKLAYIHISQVS--DGYVESLTDAFKIGDIVRAKVISYTD---PLQLSTKGKDLGVIYAMcSRCRTPLVK 161

                        170       180
                 ....*....|....*....|
6D6R_I       169 ISWCEMQCPKTHTKEFRKVA 188
Cdd:PRK09521 162 KGENELKCPNCGNIETRKLS 181
EXOSC1 pfam10447
Exosome component EXOSC1/CSL4; This family of proteins are components of the exosome 3'->5' ...
 66-137 3.75e-13

Exosome component EXOSC1/CSL4; This 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.


Pssm-ID: 402191  Cd Length: 112  Bit Score: 62.90  E-value: 3.75e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6R_I         66 LPDVGAIVTCKVSSINSRFAKVHIL--------------------YVGSMP--------------------LKNSFRGTI 105
Cdd:pfam10447   1 LPKEGDVVLARVTRLSQQQANVEILsvegennvlgdsgvgsngegAVASIPagggldilfsvstvasqssdLGETFKGII 80

                          90       100       110
                  ....*....|....*....|....*....|..
6D6R_I        106 RKEDVRATEKDKVEIYKSFRPGDIVLAKVISL 137
Cdd:pfam10447  81 RSQDVRATERDRVKVIEMFRPGDIVRAQVISL 112
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 10-45 1.42e-08

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: 48.90  E-value: 1.42e-08
                          10        20        30
                  ....*....|....*....|....*....|....*.
6D6R_I         10 CIPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMK 45
Cdd:pfam14382   2 VLPGERLGSDEEYMPGHGTYVRDGNIYASVAGTVEI 37
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
69-148 4.77e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 39.89  E-value: 4.77e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6R_I          69 VGAIVTCKVSSINSRFAKVHILyvgsmplkNSFRGTIRKEDVraTEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYLLTT 148
Cdd:smart00316   2 VGDVVEGTVTEITPGGAFVDLG--------NGVEGLIPISEL--SDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 64-136 1.43e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 38.61  E-value: 1.43e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6R_I        64 QLLPD----------VGAIVTCKVSSINSRFAKVHilyvgsmpLKNSFRGTIRKEDVratEKDKVE-IYKSFRPGDIVLA 132
Cdd:PRK06299 445 QLEEDpfeefakkhkKGSIVTGTVTEVKDKGAFVE--------LEDGVEGLIRASEL---SRDRVEdATEVLKVGDEVEA 513


                 ....
6D6R_I       133 KVIS 136
Cdd:PRK06299 514 KVIN 517
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 70-137 2.21e-03

S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 35.32  E-value: 2.21e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
6D6R_I       70 GAIVTCKVSSINSRFAKVHilyvgsmpLKNSFRGTIRKEDVratEKDKVE-IYKSFRPGDIVLAKVISL 137
Cdd:cd05691   1 GSIVTGKVTEVDAKGATVK--------LGDGVEGFLRAAEL---SRDRVEdATERFKVGDEVEAKITNV 58
 
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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