1HWQ

SOLUTION STRUCTURE OF THE VS RIBOZYME SUBSTRATE STEM-LOOP


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A pH controlled conformational switch in the cleavage site of the VS ribozyme substrate RNA.

Flinders, J.Dieckmann, T.

(2001) J Mol Biol 308: 665-679

  • DOI: https://doi.org/10.1006/jmbi.2001.4627
  • Primary Citation of Related Structures:  
    1HWQ

  • PubMed Abstract: 

    The VS ribozyme is a 154 nucleotide sequence found in certain natural strains of Neurospora. The RNA can be divided into a substrate and a catalytic domain. Here we present the solution structure of the substrate RNA that is cleaved in a trans reaction by the catalytic domain in the presence of Mg2+. The 30 nucleotide substrate RNA forms a compact helix capped by a flexible loop. The cleavage site bulge contains three non-canonical base-pairs, including an A+.C pair with a protonated adenine. This adenine (A622) is a pH controlled conformational switch that opens up the internal loop at higher pH. The possible significance of this switch for substrate recognition and cleavage is discussed.


  • Organizational Affiliation

    Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA.


Macromolecules
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Entity ID: 1
MoleculeChains LengthOrganismImage
VS RIBOZYME SUBSTRATE RNA30N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-05-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-05-22
    Changes: Data collection