Crystal Structure of Plautia Stali Intestine Virus Intergenic Region Internal Ribosome Entry Site Ribosomal Binding Domain RNA at 3.1 Angstroms

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.253 

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Structural basis for ribosome recruitment and manipulation by a viral IRES RNA

Pfingsten, J.S.Costantino, D.A.Kieft, J.S.

(2006) Science 314: 1450-1454

  • DOI: https://doi.org/10.1126/science.1133281
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Canonical cap-dependent translation initiation requires a large number of protein factors that act in a stepwise assembly process. In contrast, internal ribosomal entry sites (IRESs) are cis-acting RNAs that in some cases completely supplant these factors by recruiting and activating the ribosome using a single structured RNA. Here we present the crystal structures of the ribosome-binding domain from a Dicistroviridae intergenic region IRES at 3.1 angstrom resolution, providing a view of the prefolded architecture of an all-RNA translation initiation apparatus. Docking of the structure into cryo-electron microscopy reconstructions of an IRES-ribosome complex suggests a model for ribosome manipulation by a dynamic IRES RNA.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Colorado at Denver and Health Sciences Center, Mail Stop 8101, Post Office Box 6511, Aurora, CO 80045, USA.

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Entity ID: 1
MoleculeChains LengthOrganismImage
Ribosomal Binding Domain of the IRES RNAA,
B [auth M]
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.253 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.57α = 90
b = 133.57β = 90
c = 160.425γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references