2PN3

Crystal Structure of Hepatitis C Virus IRES Subdomain IIa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of hepatitis C virus IRES subdomain IIa.

Zhao, Q.Han, Q.Kissinger, C.R.Hermann, T.Thompson, P.A.

(2008) Acta Crystallogr.,Sect.D 64: 436-443

  • DOI: 10.1107/S0907444908002011
  • Primary Citation of Related Structures:  2PN4

  • PubMed Abstract: 
  • The hepatitis C (HCV) internal ribosome entry site (IRES) element plays a central role in cap-independent translation of the viral genomic RNA. The unique conformation of IRES domain II is critical for 80S ribosomal assembly and initiation of viral t ...

    The hepatitis C (HCV) internal ribosome entry site (IRES) element plays a central role in cap-independent translation of the viral genomic RNA. The unique conformation of IRES domain II is critical for 80S ribosomal assembly and initiation of viral translation. Here, the crystal structure of subdomain IIa of the HCV IRES has been determined at 2.3 A resolution, revealing the positions of divalent metal ions and complex inter-strand interactions that stabilize the L-shaped conformation of the RNA. The presence of divalent metal ions was necessary for crystal formation. Magnesium ions occupy specific sites that appear to be critical for the formation of the folded conformation. Subdomain IIa also was crystallized in the presence of strontium, which improved the diffraction quality of the crystals and the ability to identify interactions of the RNA with metal ions and tightly bound water molecules. The hinge region and noncanonical G-U base-pair motifs are stabilized by divalent metal ions and provide unique structural features that are potential interaction sites for small-molecule ligands. The information obtained from the crystal structure provides a basis for structure-guided design of HCV translation inhibitors targeting disruption of ribosomal assembly.


    Organizational Affiliation

    Department of Structural Chemistry, Anadys Pharmaceuticals Inc., 3115 Merryfield Row, San Diego, CA 92121, USA. qiangzhao@hotmail.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP*AP*CP*GP*CP*C)-3'A24N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*GP*CP*GP*(5BU)P*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*(5BU)P*CP*CP*GP*G)-3'B20N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5BU
Query on 5BU
B
RNA LINKINGC9 H12 Br N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.229 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 48.945α = 90.00
b = 48.945β = 90.00
c = 120.942γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
REFMACrefinement
APSdata collection
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance