1KH6

Crystal Structure of an RNA Tertiary Domain Essential to HCV IRES-mediated Translation Initiation.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.283 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation.

Kieft, J.S.Zhou, K.Grech, A.Jubin, R.Doudna, J.A.

(2002) Nat.Struct.Mol.Biol. 9: 370-374

  • DOI: 10.1038/nsb781

  • PubMed Abstract: 
  • The hepatitis C virus (HCV) internal ribosome entry site (IRES) RNA drives internal initiation of viral protein synthesis during host cell infection. In the tertiary structure of the IRES RNA, two helical junctions create recognition sites for direct ...

    The hepatitis C virus (HCV) internal ribosome entry site (IRES) RNA drives internal initiation of viral protein synthesis during host cell infection. In the tertiary structure of the IRES RNA, two helical junctions create recognition sites for direct binding of the 40S ribosomal subunit and eukaryotic initiation factor 3 (eIF3). The 2.8 A resolution structure of the IIIabc four-way junction, which is critical for binding eIF3, reveals how junction nucleotides interact with an adjacent helix to position regions directly involved in eIF3 recognition. Two of the emergent helices stack to form a nearly continuous A-form duplex, while stacking of the other two helices is interrupted by the insertion of junction residues into the helix minor groove. This distorted stack probably serves as an important recognition surface for the translational machinery.


    Organizational Affiliation

    [1] Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114 USA. [2] Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8114 USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
JIIIabcA53N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5BU
Query on 5BU
A
RNA LINKINGC9 H12 Br N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.283 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 66.532α = 90.00
b = 66.532β = 90.00
c = 95.850γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-04-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-02-08
    Type: Database references, Structure summary