4WTM

CRYSTAL STRUCTURE OF HCV NS5B GENOTYPE 2A JFH-1 ISOLATE WITH S15G E86Q E87Q C223H V321I MUTATIONS IN COMPLEX WITH RNA TEMPLATE 5'-UAGG, RNA PRIMER 5'-PCC, MN2+, AND UDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for RNA replication by the hepatitis C virus polymerase.

Appleby, T.C.Perry, J.K.Murakami, E.Barauskas, O.Feng, J.Cho, A.Fox, D.Wetmore, D.R.McGrath, M.E.Ray, A.S.Sofia, M.J.Swaminathan, S.Edwards, T.E.

(2015) Science 347: 771-775

  • DOI: 10.1126/science.1259210
  • Primary Citation of Related Structures:  
    4WTI, 4WTJ, 4WTK, 4WTL, 4WTM, 4WTA, 4WTC, 4WTD, 4WTE, 4WTF

  • PubMed Abstract: 
  • Nucleotide analog inhibitors have shown clinical success in the treatment of hepatitis C virus (HCV) infection, despite an incomplete mechanistic understanding of NS5B, the viral RNA-dependent RNA polymerase. Here we study the details of HCV RNA repl ...

    Nucleotide analog inhibitors have shown clinical success in the treatment of hepatitis C virus (HCV) infection, despite an incomplete mechanistic understanding of NS5B, the viral RNA-dependent RNA polymerase. Here we study the details of HCV RNA replication by determining crystal structures of stalled polymerase ternary complexes with enzymes, RNA templates, RNA primers, incoming nucleotides, and catalytic metal ions during both primed initiation and elongation of RNA synthesis. Our analysis revealed that highly conserved active-site residues in NS5B position the primer for in-line attack on the incoming nucleotide. A β loop and a C-terminal membrane-anchoring linker occlude the active-site cavity in the apo state, retract in the primed initiation assembly to enforce replication of the HCV genome from the 3' terminus, and vacate the active-site cavity during elongation. We investigated the incorporation of nucleotide analog inhibitors, including the clinically active metabolite formed by sofosbuvir, to elucidate key molecular interactions in the active site.


    Organizational Affiliation

    Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA. todd.appleby@gilead.com tedwards@be4.com.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymeraseA580Hepatitis C virus JFH-1Mutation(s): 5 
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))
Explore Q99IB8 
Go to UniProtKB:  Q99IB8
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    RNA TEMPLATE UAGGT4synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      RNA PRIMER CCP2synthetic construct
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      UDP
      Query on UDP

      Download CCD File 
      A
      URIDINE-5'-DIPHOSPHATE
      C9 H14 N2 O12 P2
      XCCTYIAWTASOJW-XVFCMESISA-N
       Ligand Interaction
      MN
      Query on MN

      Download CCD File 
      A
      MANGANESE (II) ION
      Mn
      WAEMQWOKJMHJLA-UHFFFAOYSA-N
       Ligand Interaction
      CL
      Query on CL

      Download CCD File 
      A
      CHLORIDE ION
      Cl
      VEXZGXHMUGYJMC-UHFFFAOYSA-M
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.15 Å
      • R-Value Free: 0.216 
      • R-Value Work: 0.185 
      • R-Value Observed: 0.186 
      • Space Group: P 65
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 140.37α = 90
      b = 140.37β = 90
      c = 92.43γ = 120
      Software Package:
      Software NamePurpose
      XSCALEdata scaling
      REFMACrefinement
      PDB_EXTRACTdata extraction
      PHASERphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2015-02-11
        Type: Initial release
      • Version 1.1: 2015-02-25
        Changes: Database references
      • Version 1.2: 2017-09-27
        Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy