3T4B

Crystal Structure of the HCV IRES pseudoknot domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the HCV IRES central domain reveals strategy for start-codon positioning.

Berry, K.E.Waghray, S.Mortimer, S.A.Bai, Y.Doudna, J.A.

(2011) Structure 19: 1456-1466

  • DOI: 10.1016/j.str.2011.08.002

  • PubMed Abstract: 
  • Translation of hepatitis C viral proteins requires an internal ribosome entry site (IRES) located in the 5' untranslated region of the viral mRNA. The core domain of the hepatitis C virus (HCV) IRES contains a four-way helical junction that is integr ...

    Translation of hepatitis C viral proteins requires an internal ribosome entry site (IRES) located in the 5' untranslated region of the viral mRNA. The core domain of the hepatitis C virus (HCV) IRES contains a four-way helical junction that is integrated within a predicted pseudoknot. This domain is required for positioning the mRNA start codon correctly on the 40S ribosomal subunit during translation initiation. Here, we present the crystal structure of this RNA, revealing a complex double-pseudoknot fold that establishes the alignment of two helical elements on either side of the four-helix junction. The conformation of this core domain constrains the open reading frame's orientation for positioning on the 40S ribosomal subunit. This structure, representing the last major domain of HCV-like IRESs to be determined at near-atomic resolution, provides the basis for a comprehensive cryoelectron microscopy-guided model of the intact HCV IRES and its interaction with 40S ribosomal subunits.


    Organizational Affiliation

    Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
HCV IRES pseudoknot domain plus crystallization moduleA84synthetic constructHepatitis C virus ED43
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
A23
Query on A23
A
RNA LINKINGC10 H13 N5 O9 P2A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.221 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 113.390α = 90.00
b = 113.390β = 90.00
c = 88.220γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
SOLVEphasing
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-12
    Type: Initial release
  • Version 1.1: 2011-10-26
    Type: Database references
  • Version 1.2: 2011-11-23
    Type: Other
  • Version 1.3: 2017-06-28
    Type: Database references, Derived calculations, Source and taxonomy, Structure summary