1D0U

SOLUTION STRUCTURE OF AN RNA BINDING SITE FOR PHAGE MS2 COAT PROTEIN


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 111 
  • Conformers Submitted: 23 
  • Selection Criteria: back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with the least restraint violations, structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Phosphorothioate substitution can substantially alter RNA conformation.

Smith, J.S.Nikonowicz, E.P.

(2000) Biochemistry 39: 5642-5652

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Phosphorothioate substitution-interference experiments, routinely used to stereospecifically identify phosphoryl oxygen sites that participate in RNA-ligand binding and RNA-directed catalysis, rest in their interpretation on the untested assumption t ...

    Phosphorothioate substitution-interference experiments, routinely used to stereospecifically identify phosphoryl oxygen sites that participate in RNA-ligand binding and RNA-directed catalysis, rest in their interpretation on the untested assumption that substitution does not alter the conformation of the modified molecule from its biologically active state. Using NMR spectroscopy, we have tested this assumption by determining the structural effect of stereospecific phosphorothioate substitution at five positions in an RNA hairpin containing the binding site for bacteriophage MS2 capsid protein. At most sites, substitution has little or no effect, causing minor perturbations in the phosphate backbone and increasing the stacking among nucleotides in the hairpin loop. At one site, however, phosphorothioate substitution causes an unpaired adenine necessary for formation of the capsid protein-RNA complex to loop out of the RNA helix into the major groove. These results indicate that phosphorothioate substitution can substantially alter the conformation of RNA at positions of irregular secondary structure, complicating the use of substitution-interference experiments to study RNA structure and function.


    Organizational Affiliation

    Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, USA.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
PHAGE MS2 RNA BINDING SITEA21N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 111 
  • Conformers Submitted: 23 
  • Selection Criteria: back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with the least restraint violations, structures with the lowest energy 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance