5V3I

Crystal structure of the VS ribozyme - wild-type C634

  • Classification: RNA
  • Organism(s): Neurospora

  • Deposited: 2017-03-07 Released: 2017-07-05 
  • Deposition Author(s): DasGupta, S., Suslov, N.B., Piccirilli, J.A.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.293 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for Substrate Helix Remodeling and Cleavage Loop Activation in the Varkud Satellite Ribozyme.

DasGupta, S.Suslov, N.B.Piccirilli, J.A.

(2017) J. Am. Chem. Soc. 139: 9591-9597

  • DOI: 10.1021/jacs.7b03655

  • PubMed Abstract: 
  • The Varkud satellite (VS) ribozyme catalyzes site-specific RNA cleavage and ligation reactions. Recognition of the substrate involves a kissing loop interaction between the substrate and the catalytic domain of the ribozyme, resulting in a rearrangem ...

    The Varkud satellite (VS) ribozyme catalyzes site-specific RNA cleavage and ligation reactions. Recognition of the substrate involves a kissing loop interaction between the substrate and the catalytic domain of the ribozyme, resulting in a rearrangement of the substrate helix register into a so-called "shifted" conformation that is critical for substrate binding and activation. We report a 3.3 √Ö crystal structure of the complete ribozyme that reveals the active, shifted conformation of the substrate, docked into the catalytic domain of the ribozyme. Comparison to previous NMR structures of isolated, inactive substrates provides a physical description of substrate remodeling, and implicates roles for tertiary interactions in catalytic activation of the cleavage loop. Similarities to the hairpin ribozyme cleavage loop activation suggest general strategies to enhance fidelity in RNA folding and ribozyme cleavage.


    Organizational Affiliation

    Department of Chemistry, and ‡Department of Biochemistry and Molecular Biology, The University of Chicago , Chicago, Illinois 60637, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
VS Ribozyme RNAA186Neurospora
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.293 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.216 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 104.306α = 90.00
b = 104.306β = 90.00
c = 211.906γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesRO1AI081987

Revision History 

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2017-08-02
    Type: Author supporting evidence, Database references