2ESE

Structure of the SAM domain of Vts1p in complex with RNA

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

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This is version 1.3 of the entry. See complete history. 


Literature

Shape-specific recognition in the structure of the Vts1p SAM domain with RNA.

Oberstrass, F.C., Lee, A., Stefl, R., Janis, M., Chanfreau, G., Allain, F.H.

(2006) Nat Struct Mol Biol 13: 160-167

  • DOI: 10.1038/nsmb1038
  • Primary Citation of Related Structures:  
    2ES5, 2ES6, 2ESE

  • PubMed Abstract: 

    • Although the abundant sterile alpha motif (SAM) domain was originally classified as a protein-protein interaction domain, it has recently been shown that certain SAM domains have the ability to bind RNA, defining a new type of post-transcriptional gene regulator ...

    Although the abundant sterile alpha motif (SAM) domain was originally classified as a protein-protein interaction domain, it has recently been shown that certain SAM domains have the ability to bind RNA, defining a new type of post-transcriptional gene regulator. To further understand the function of SAM-RNA recognition, we determined the solution structures of the SAM domain of the Saccharomyces cerevisiae Vts1p (Vts1p-SAM) and the Smaug response element (SRE) stem-loop RNA as a complex and in isolation. The structures show that Vts1p-SAM recognizes predominantly the shape of the SRE rather than its sequence, with the exception of a G located at the tip of the pentaloop. Using microarray gene profiling, we identified several genes in S. cerevisiae that seem to be regulated by Vts1p and contain one or more copies of the SRE.

    Organizational Affiliation: 

    Institute for Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zurich, Switzerland.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Vts1pB [auth A]101Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q08831 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08831 
Go to UniProtKB:  Q08831
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08831
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(*GP*GP*AP*GP*AP*GP*GP*CP*UP*CP*UP*GP*GP*CP*AP*GP*CP*UP*UP*UP*UP*CP*C)-3'A [auth B]23N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 2ESE Olderado

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2005-10-26 
  • Released Date: 2006-01-24 
    • Deposition Author(s): Allain, F.H.T.

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-24
    Type: Initial release
  • Version 1.1: 2007-10-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-09
    Changes: Data collection, Database references, Derived calculations