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Conserved domains on  [gi|2217267790|ref|XP_047277451|]
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Y-box-binding protein 1 isoform X1 [Homo sapiens]

Protein Classification

cold shock domain-containing protein( domain architecture ID 10138668)

cold shock domain-containing protein similar to mammalian calcium-regulated heat-stable protein 1, which binds mRNA and regulates the stability of target mRNA

CATH:  2.40.50.140
Gene Ontology:  GO:0003676
PubMed:  2184368|10377894|10322168
SCOP:  4001909

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 61-90 4.27e-12

Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.


:

Pssm-ID: 239905  Cd Length: 65  Bit Score: 60.28  E-value: 4.27e-12
                          10        20        30
                  ....*....|....*....|....*....|
gi 2217267790  61 GTVKWFNVRNGYGFINRNDTKEDVFVHQGA 90
Cdd:cd04458     3 GTVKWFDDEKGFGFITPDDGGEDVFVHISA 32
 
Name Accession Description Interval E-value
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 61-90 4.27e-12

Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.


Pssm-ID: 239905  Cd Length: 65  Bit Score: 60.28  E-value: 4.27e-12
                          10        20        30
                  ....*....|....*....|....*....|
gi 2217267790  61 GTVKWFNVRNGYGFINRNDTKEDVFVHQGA 90
Cdd:cd04458     3 GTVKWFDDEKGFGFITPDDGGEDVFVHISA 32
CSD pfam00313
'Cold-shock' DNA-binding domain;
59-90 1.91e-11

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 58.41  E-value: 1.91e-11
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2217267790  59 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQGA 90
Cdd:pfam00313   1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSA 32
CspC COG1278
Cold shock protein, CspA family [Transcription];
61-87 3.68e-09

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 52.12  E-value: 3.68e-09
                          10        20
                  ....*....|....*....|....*..
gi 2217267790  61 GTVKWFNVRNGYGFINRNDTKEDVFVH 87
Cdd:COG1278     4 GTVKWFNAEKGFGFITPDDGGEDVFVH 30
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 61-90 2.92e-07

Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.


Pssm-ID: 214633 [Multi-domain]  Cd Length: 64  Bit Score: 46.82  E-value: 2.92e-07
                           10        20        30
                   ....*....|....*....|....*....|
gi 2217267790   61 GTVKWFNvrNGYGFINRNDTKEDVFVHQGA 90
Cdd:smart00357   2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQ 29
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
55-90 3.76e-06

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 43.81  E-value: 3.76e-06
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 2217267790  55 IATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQGA 90
Cdd:PRK10354    1 MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSA 36
 
Name Accession Description Interval E-value
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 61-90 4.27e-12

Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.


Pssm-ID: 239905  Cd Length: 65  Bit Score: 60.28  E-value: 4.27e-12
                          10        20        30
                  ....*....|....*....|....*....|
gi 2217267790  61 GTVKWFNVRNGYGFINRNDTKEDVFVHQGA 90
Cdd:cd04458     3 GTVKWFDDEKGFGFITPDDGGEDVFVHISA 32
CSD pfam00313
'Cold-shock' DNA-binding domain;
59-90 1.91e-11

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 58.41  E-value: 1.91e-11
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2217267790  59 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQGA 90
Cdd:pfam00313   1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSA 32
CspC COG1278
Cold shock protein, CspA family [Transcription];
61-87 3.68e-09

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 52.12  E-value: 3.68e-09
                          10        20
                  ....*....|....*....|....*..
gi 2217267790  61 GTVKWFNVRNGYGFINRNDTKEDVFVH 87
Cdd:COG1278     4 GTVKWFNAEKGFGFITPDDGGEDVFVH 30
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 61-90 2.92e-07

Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.


Pssm-ID: 214633 [Multi-domain]  Cd Length: 64  Bit Score: 46.82  E-value: 2.92e-07
                           10        20        30
                   ....*....|....*....|....*....|
gi 2217267790   61 GTVKWFNvrNGYGFINRNDTKEDVFVHQGA 90
Cdd:smart00357   2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQ 29
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
55-90 3.76e-06

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 43.81  E-value: 3.76e-06
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 2217267790  55 IATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQGA 90
Cdd:PRK10354    1 MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSA 36
PRK09890 PRK09890
cold shock protein CspG; Provisional
 55-94 4.31e-06

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 43.60  E-value: 4.31e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2217267790  55 IATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQGAEAAN 94
Cdd:PRK09890    1 MSNKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSN 40
cspE PRK09507
cold shock-like protein CspE;
57-94 5.22e-06

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 43.49  E-value: 5.22e-06
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2217267790  57 TKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQGAEAAN 94
Cdd:PRK09507    2 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN 39
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 58-94 4.52e-04

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 38.13  E-value: 4.52e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2217267790  58 KVLGTVKWFNVRNGYGFINRNDTKEDVFVHQGAEAAN 94
Cdd:PRK10943    3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGN 39
PRK09937 PRK09937
cold shock-like protein CspD;
61-87 4.84e-03

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 35.09  E-value: 4.84e-03
                          10        20
                  ....*....|....*....|....*..
gi 2217267790  61 GTVKWFNVRNGYGFINRNDTKEDVFVH 87
Cdd:PRK09937    4 GTVKWFNNAKGFGFICPEGGGEDIFAH 30
 
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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