Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 14.26 kDa 
• Atom Count: 932 
• Modelled Residue Count: 44 
• Deposited Residue Count: 44 
• Unique nucleic acid chains: 2

2PN3

Crystal Structure of Hepatitis C Virus IRES Subdomain IIa

• PDB DOI: 10.2210/pdb2PN3/pdb
• NDB: AR0077

• Classification: RNA
• Mutation(s): No 


• Deposited: 2007-04-23 Released: 2008-04-01 
• Deposition Author(s): Zhao, Q., Han, Q., Kissinger, C.R., Hermann, T., Thompson, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.283 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 

Literature

Structure of hepatitis C virus IRES subdomain IIa.

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

(2008) Acta Crystallogr D Biol Crystallogr 64: 436-443

• PubMed: 18391410 
• DOI: 10.1107/S0907444908002011
• Primary Citation of Related Structures:  
  2PN3, 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 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.

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Organizational Affiliation: 

Department of Structural Chemistry, Anadys Pharmaceuticals Inc., 3115 Merryfield Row, San Diego, CA 92121, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
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'	A	24	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
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'	B	20	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.283 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.945	α = 90
b = 48.945	β = 90
c = 120.942	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
APS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-04-23 
• Released Date: 2008-04-01 
Deposition Author(s): Zhao, Q., Han, Q., Kissinger, C.R., Hermann, T., Thompson, P.A.

Revision History  

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