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Conserved domains on  [gi|971460855|ref|NP_001305291|]
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exosome complex component CSL4 isoform b [Homo sapiens]

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 ...
 48-129 1.73e-48

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: 152.01  E-value: 1.73e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971460855  48 GAVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSnYLLTTAENELG 127
Cdd:cd05791   12 ARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASS-YYLSTAENELG 90


                 ..
gi 971460855 128 VV 129
Cdd:cd05791   91 VV 92
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 8-43 5.82e-09

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: 49.28  E-value: 5.82e-09
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 971460855    8 CIPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMK 43
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 ...
 48-129 1.73e-48

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: 152.01  E-value: 1.73e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971460855  48 GAVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSnYLLTTAENELG 127
Cdd:cd05791   12 ARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASS-YYLSTAENELG 90


                 ..
gi 971460855 128 VV 129
Cdd:cd05791   91 VV 92
Csl4 COG1096
Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...
 9-161 3.38e-20

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: 82.64  E-value: 3.38e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971460855   9 IPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKSSEN----------------------GAVSSINSRFAKVHILYVG 66
Cdd:COG1096   10 LPGDVLAVIEEFLPGEGTYEEDGKIRAAVVGKVVIDDKNrvisvkpkkkpppvpkkgdiviGEVVDVRESMALVKIYAIE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971460855  67 SM--PLKNSFRGTIRKEDVRATEKDKveIYKSFRPGDIVLAKVISLGdaqSNYLLTTAENELGVVVAH-SESGIQMVPIS 143
Cdd:COG1096   90 GNerELPSSFSGIIHISQVSDSYVKD--LSDEFRVGDIVRAKVISTL---PPIQLSIKEPDLGVIKAKcSKCGSPLVKDG 164

                        170
                 ....*....|....*...
gi 971460855 144 wCEMQCPKTHTKEFRKVA 161
Cdd:COG1096  165 -DKLKCPNCGNVEKRKLS 181
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 10-161 1.15e-14

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 68.08  E-value: 1.15e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971460855  10 PGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKSSEN----------------------GAVSSINSRFAKVHILYV-- 65
Cdd:PRK09521  10 PGDYLAVIEEYLPGEGTYEDNGEVYASVVGKVFIDDINrkisvipfkktppllkkgdivyGRVVDVKEQRALVRIVSIeg 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971460855  66 GSMPLKNSFRGTIRKEDVRatEKDKVEIYKSFRPGDIVLAKVISLGDaqsNYLLTTAENELGVVVAH-SESGIQMVPISW 144
Cdd:PRK09521  90 SERELATSKLAYIHISQVS--DGYVESLTDAFKIGDIVRAKVISYTD---PLQLSTKGKDLGVIYAMcSRCRTPLVKKGE 164

                        170
                 ....*....|....*..
gi 971460855 145 CEMQCPKTHTKEFRKVA 161
Cdd:PRK09521 165 NELKCPNCGNIETRKLS 181
EXOSC1 pfam10447
Exosome component EXOSC1/CSL4; This family of proteins are components of the exosome 3'->5' ...
 74-110 2.48e-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: 2.48e-13
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 971460855   74 FRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISL 110
Cdd:pfam10447  76 FKGIIRSQDVRATERDRVKVIEMFRPGDIVRAQVISL 112
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 8-43 5.82e-09

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: 49.28  E-value: 5.82e-09
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 971460855    8 CIPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMK 43
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 ...
 48-129 1.73e-48

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: 152.01  E-value: 1.73e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971460855  48 GAVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSnYLLTTAENELG 127
Cdd:cd05791   12 ARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASS-YYLSTAENELG 90


                 ..
gi 971460855 128 VV 129
Cdd:cd05791   91 VV 92
S1_Rrp4_like cd04454
S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in ...
 48-129 2.58e-25

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: 92.61  E-value: 2.58e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971460855  48 GAVSSINSRFAKVHILYvgsmplknsfRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAqSNYLLTTAENELG 127
Cdd:cd04454   12 GIVTEVNSRFWKVDILS----------RGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTADNELG 80


                 ..
gi 971460855 128 VV 129
Cdd:cd04454   81 VI 82
Csl4 COG1096
Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...
 9-161 3.38e-20

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: 82.64  E-value: 3.38e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971460855   9 IPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKSSEN----------------------GAVSSINSRFAKVHILYVG 66
Cdd:COG1096   10 LPGDVLAVIEEFLPGEGTYEEDGKIRAAVVGKVVIDDKNrvisvkpkkkpppvpkkgdiviGEVVDVRESMALVKIYAIE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971460855  67 SM--PLKNSFRGTIRKEDVRATEKDKveIYKSFRPGDIVLAKVISLGdaqSNYLLTTAENELGVVVAH-SESGIQMVPIS 143
Cdd:COG1096   90 GNerELPSSFSGIIHISQVSDSYVKD--LSDEFRVGDIVRAKVISTL---PPIQLSIKEPDLGVIKAKcSKCGSPLVKDG 164

                        170
                 ....*....|....*...
gi 971460855 144 wCEMQCPKTHTKEFRKVA 161
Cdd:COG1096  165 -DKLKCPNCGNVEKRKLS 181
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 10-161 1.15e-14

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 68.08  E-value: 1.15e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971460855  10 PGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKSSEN----------------------GAVSSINSRFAKVHILYV-- 65
Cdd:PRK09521  10 PGDYLAVIEEYLPGEGTYEDNGEVYASVVGKVFIDDINrkisvipfkktppllkkgdivyGRVVDVKEQRALVRIVSIeg 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971460855  66 GSMPLKNSFRGTIRKEDVRatEKDKVEIYKSFRPGDIVLAKVISLGDaqsNYLLTTAENELGVVVAH-SESGIQMVPISW 144
Cdd:PRK09521  90 SERELATSKLAYIHISQVS--DGYVESLTDAFKIGDIVRAKVISYTD---PLQLSTKGKDLGVIYAMcSRCRTPLVKKGE 164

                        170
                 ....*....|....*..
gi 971460855 145 CEMQCPKTHTKEFRKVA 161
Cdd:PRK09521 165 NELKCPNCGNIETRKLS 181
EXOSC1 pfam10447
Exosome component EXOSC1/CSL4; This family of proteins are components of the exosome 3'->5' ...
 74-110 2.48e-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: 2.48e-13
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 971460855   74 FRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISL 110
Cdd:pfam10447  76 FKGIIRSQDVRATERDRVKVIEMFRPGDIVRAQVISL 112
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 8-43 5.82e-09

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: 49.28  E-value: 5.82e-09
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 971460855    8 CIPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMK 43
Cdd:pfam14382   2 VLPGERLGSDEEYMPGHGTYVRDGNIYASVAGTVEI 37
 
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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