1JZC

THE SOLUTION STRUCTURE OF THE MUTANT 5'AUG3' TRILOOP IN THE RNA PROMOTER REGION OF THE BROME MOSAIC VIRUS GENOMIC (+)-RNA

  • Classification: RNA

  • Deposited: 2001-09-14 Released: 2003-10-07 
  • Deposition Author(s): Kim, C.-H., Kao, C.C.

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 17 
  • Conformers Submitted: 
  • Selection Criteria: a strucutre averaged over these 17 calculated structures. 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A mutant viral RNA promoter with an altered conformation retains efficient recognition by a viral RNA replicase through a solution-exposed adenine

Kim, C.-H.Kao, C.C.

(2001) RNA 7: 1476-1485


  • PubMed Abstract: 
  • Brome mosaic virus (BMV) genomic minus-strand RNA synthesis requires an RNA motif named stem-loop C (SLC). An NMR-derived solution structure of SLC was reported by Kim et al. (Nature Struc Biol, 2000, 7:415-423) to contain three replicase-recognition ...

    Brome mosaic virus (BMV) genomic minus-strand RNA synthesis requires an RNA motif named stem-loop C (SLC). An NMR-derived solution structure of SLC was reported by Kim et al. (Nature Struc Biol, 2000, 7:415-423) to contain three replicase-recognition elements, the most important of which is a stable stem with a terminal trinucleotide loop, 5'AUA3'. The 5'-most adenine of the triloop is rigidly fixed to the stem helix by interactions that require the 3'-most adenine, which is called a clamped adenine motif. However, a change of the 3' adenine to guanine (5'AUG3') unexpectedly directed RNA synthesis at 130% of wild type (Kim et al., Nature Struc Biol, 2000, 7:415-423). To understand how RNA with the AUG mutation maintains interaction with the BMV replicase, we used NMR and other biophysical techniques to elucidate the solution conformation of a 13-nt RNA containing the AUG triloop, called S-AUG. We found that S-AUG has a drastically different loop conformation in comparison to the wild type, as evidenced by an unusual C x G loop-closing base pair. Despite the conformational change, S-AUG maintains a solution-exposed adenine similar to the clamped adenine motif found in the wild type. Biochemical studies of the 5'AUG3' loop with various substitutions in the context of the whole SLC construct confirm that the clamped adenine motif exists in S-AUG remains a primary structural feature required for RNA synthesis by the BMV replicase.


    Related Citations: 
    • Structural and Thermodynamic Studies on Mutant RNA motifs that impair the Specificity between a Viral Replicase and its Promoter
      Kim, C.-H.,Tinoco Jr., I.
      (2001) J.Mol.Biol. 307: 827
    • RNA motifs that determine specificity between a viral replicase and its promoter
      Kim, C.-H.,Kao, C.C.,Tinoco Jr., I.
      (2000) Nat.Struct.Mol.Biol. 7: 415


    Organizational Affiliation

    Department of Chemistry, University of California, Berkeley, 94720-1460, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*GP*GP*UP*GP*CP*AP*UP*GP*GP*CP*AP*CP*C)-3'A13N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 17 
  • Conformers Submitted: 
  • Selection Criteria: a strucutre averaged over these 17 calculated structures. 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2001-09-14 
  • Released Date: 2003-10-07 
  • Deposition Author(s): Kim, C.-H., Kao, C.C.

Revision History 

  • Version 1.0: 2003-10-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance