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 
  • R-Value Observed: 0.223 

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
  • Primary Citation of Related Structures:  
    3T4B

  • 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 integrated within a predicted pseudoknot ...

    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 nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
HCV IRES pseudoknot domain plus crystallization moduleA84synthetic constructHepatitis C virus ED43
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.39α = 90
b = 113.39β = 90
c = 88.22γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
SOLVEphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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