3B31

Crystal structure of domain III of the Cricket Paralysis Virus IRES RNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


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

Literature

tRNA-mRNA mimicry drives translation initiation from a viral IRES.

Costantino, D.A., Pfingsten, J.S., Rambo, R.P., Kieft, J.S.

(2008) Nat.Struct.Mol.Biol. 15: 57-64

  • DOI: 10.1038/nsmb1351

  • PubMed Abstract: 

    • Internal ribosome entry site (IRES) RNAs initiate protein synthesis in eukaryotic cells by a noncanonical cap-independent mechanism. IRESes are critical for many pathogenic viruses, but efforts to understand their function are complicated by the dive ...

    Internal ribosome entry site (IRES) RNAs initiate protein synthesis in eukaryotic cells by a noncanonical cap-independent mechanism. IRESes are critical for many pathogenic viruses, but efforts to understand their function are complicated by the diversity of IRES sequences as well as by limited high-resolution structural information. The intergenic region (IGR) IRESes of the Dicistroviridae viruses are powerful model systems to begin to understand IRES function. Here we present the crystal structure of a Dicistroviridae IGR IRES domain that interacts with the ribosome's decoding groove. We find that this RNA domain precisely mimics the transfer RNA anticodon-messenger RNA codon interaction, and its modeled orientation on the ribosome helps explain translocation without peptide bond formation. When combined with a previous structure, this work completes the first high-resolution description of an IRES RNA and provides insight into how RNAs can manipulate complex biological machines.

    Organizational Affiliation: 

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




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
RNA (29-MER)A29N/A
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*AP*AP*GP*AP*AP*AP*UP*UP*UP*AP*CP*CP*U)-3')B14N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download SDF File 
Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
IRI
Query on IRI
Download SDF File 
Download CCD File 
A
IRIDIUM HEXAMMINE ION
H18 Ir N6
CGMAOQLDNKCXGK-RIUFHJFFAL
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.239 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.724α = 90.00
b = 58.724β = 90.00
c = 98.989γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
CNSrefinement
ELVESdata reduction
MOSFLMdata reduction
PHENIXmodel building
CCP4data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description