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Conserved domains on  [gi|50511939|ref|NP_001002269|]
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exosome complex component RRP40 isoform 2 [Homo sapiens]

Protein Classification

S1 domain-containing protein( domain architecture ID 237)

S1 domain-containing protein may bind RNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 108-159 1.01e-29

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member cd05790:

Pssm-ID: 471952  Cd Length: 86  Bit Score: 103.88  E-value: 1.01e-29
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 50511939 108 RYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQA 159
Cdd:cd05790   1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNV 52
 
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 ...
 108-159 1.01e-29

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: 103.88  E-value: 1.01e-29
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 50511939 108 RYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQA 159
Cdd:cd05790   1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNV 52
 
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 ...
 108-159 1.01e-29

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: 103.88  E-value: 1.01e-29
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 50511939 108 RYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQA 159
Cdd:cd05790   1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNV 52
S1_Rrp4_like cd04454
S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in ...
 108-158 3.92e-19

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: 76.82  E-value: 3.92e-19
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 50511939 108 RYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGA-TKRNRPNVQ 158
Cdd:cd04454   1 RYLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKdKKEIRKSLQ 52
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 108-142 1.46e-03

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: 35.99  E-value: 1.46e-03
                        10        20        30
                ....*....|....*....|....*....|....*
gi 50511939 108 RYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLS 142
Cdd:cd05789   1 RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLP 35
 
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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