1TBK

NMR structure of the VS ribozyme stem-loop V RNA in the absence of multivalent ions.


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 61 
  • Conformers Submitted: 11 
  • Selection Criteria: The submitted conformer models are the 10 structures with the lowest energy (MODEL 2 -- 11) 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Nuclear Magnetic Resonance Structure of the Varkud Satellite Ribozyme Stem-Loop V RNA and Magnesium-Ion Binding from Chemical-Shift Mapping

Campbell, D.O.Legault, P.

(2005) Biochemistry 44: 4157-4170

  • DOI: 10.1021/bi047963l

  • PubMed Abstract: 
  • An important step in the substrate recognition of the Neurospora Varkud Satellite (VS) ribozyme is the formation of a magnesium-dependent loop/loop interaction between the terminal loops of stem-loops I and V. We have studied the structure of stem-lo ...

    An important step in the substrate recognition of the Neurospora Varkud Satellite (VS) ribozyme is the formation of a magnesium-dependent loop/loop interaction between the terminal loops of stem-loops I and V. We have studied the structure of stem-loop V by nuclear magnetic resonance spectroscopy and shown that it adopts a U-turn conformation, a common motif found in RNA. Structural comparisons indicate that the U-turn of stem-loop V fulfills some but not all of the structural characteristics found in canonical U-turn structures. This U-turn conformation exposes the Watson-Crick faces of the bases within stem-loop V (G697, A698, and C699) and makes them accessible for interaction with stem-loop I. Using chemical-shift mapping, we show that magnesium ions interact with the loop of the isolated stem-loop V and induce a conformational change that may be important for interaction with stem-loop I. This study expands our understanding of the role of U-turn motifs in RNA structure and function and provides insights into the mechanism of substrate recognition in the VS ribozyme.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
VS ribozyme stem-loop VA17N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 61 
  • Conformers Submitted: 11 
  • Selection Criteria: The submitted conformer models are the 10 structures with the lowest energy (MODEL 2 -- 11) 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance