1L3D

Low Resolution Crystal Structure of a Viral RNA Pseudoknot

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.271 

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This is version 1.2 of the entry. See complete history. 

Literature

Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution.

Egli, M., Minasov, G., Su, L., Rich, A.

(2002) Proc.Natl.Acad.Sci.USA 99: 4302-4307

  • DOI: 10.1073/pnas.062055599
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Many pathogenic viruses use programmed -1 ribosomal frameshifting to regulate translation of their structural and enzymatic proteins from polycistronic mRNAs. Frameshifting is commonly stimulated by a pseudoknot located downstream from a slippery seq ...

    Many pathogenic viruses use programmed -1 ribosomal frameshifting to regulate translation of their structural and enzymatic proteins from polycistronic mRNAs. Frameshifting is commonly stimulated by a pseudoknot located downstream from a slippery sequence, the latter positioned at the ribosomal A and P sites. We report here the structures of two crystal forms of the frameshifting RNA pseudoknot from beet western yellow virus at resolutions of 1.25 and 2.85 A. Because of the very high resolution of 1.25 A, ten mono- and divalent metal ions per asymmetric unit could be identified, giving insight into potential roles of metal ions in stabilizing the pseudoknot. A magnesium ion located at the junction of the two pseudoknot stems appears to play a crucial role in stabilizing the structure. Because the two crystal forms exhibit mostly unrelated packing interactions and local crystallographic disorder in the high-resolution form was resolvable, the two structures offer the most detailed view yet of the conformational preference and flexibility of an RNA pseudoknot.

    Organizational Affiliation: 

    Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
RNA pseudoknotA28N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GTP
Query on GTP
A
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.271 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 107.810α = 90.00
b = 107.810β = 90.00
c = 107.810γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-22
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance