4E7A

Crystal structure of a product state assembly of HCV NS5B genotype 2a JFH-1 isolate with beta hairpin deletion bound to primer-template RNA with a 2',3'-ddC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of hepatitis C virus polymerase in complex with primer-template RNA.

Mosley, R.T.Edwards, T.E.Murakami, E.Lam, A.M.Grice, R.L.Du, J.Sofia, M.J.Furman, P.A.Otto, M.J.

(2012) J Virol 86: 6503-6511

  • DOI: 10.1128/JVI.00386-12
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The replication of the hepatitis C viral (HCV) genome is accomplished by the NS5B RNA-dependent RNA polymerase (RdRp), for which mechanistic understanding and structure-guided drug design efforts have been hampered by its propensity to crystallize in ...

    The replication of the hepatitis C viral (HCV) genome is accomplished by the NS5B RNA-dependent RNA polymerase (RdRp), for which mechanistic understanding and structure-guided drug design efforts have been hampered by its propensity to crystallize in a closed, polymerization-incompetent state. The removal of an autoinhibitory β-hairpin loop from genotype 2a HCV NS5B increases de novo RNA synthesis by >100-fold, promotes RNA binding, and facilitated the determination of the first crystallographic structures of HCV polymerase in complex with RNA primer-template pairs. These crystal structures demonstrate the structural realignment required for primer-template recognition and elongation, provide new insights into HCV RNA synthesis at the molecular level, and may prove useful in the structure-based design of novel antiviral compounds. Additionally, our approach for obtaining the RNA primer-template-bound structure of HCV polymerase may be generally applicable to solving RNA-bound complexes for other viral RdRps that contain similar regulatory β-hairpin loops, including bovine viral diarrhea virus, dengue virus, and West Nile virus.


    Organizational Affiliation

    Pharmasset Inc, Princeton, New Jersey, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase
A
572Hepatitis C virus JFH-1Mutation(s): 2 
Gene Names: NS5B
EC: 2.7.7.48 (PDB Primary Data), 3.4.22 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
Find proteins for Q99IB8 (Hepatitis C virus genotype 2a (isolate JFH-1))
Go to UniProtKB:  Q99IB8
Protein Feature View
  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*CP*AP*UP*GP*GP*C)-D(P*(DOC))-3'P, T7N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.73α = 90
b = 142.73β = 90
c = 91.5γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2012-04-25
    Changes: Database references
  • Version 1.2: 2012-06-06
    Changes: Database references
  • Version 1.3: 2017-07-26
    Changes: Refinement description, Source and taxonomy