4WTG

CRYSTAL STRUCTURE OF HCV NS5B GENOTYPE 2A JFH-1 ISOLATE WITH S15G E86Q E87Q C223H V321I MUTATIONS AND DELTA8 BETA HAIRPIN LOOP DELETION IN COMPLEX WITH SOFOSBUVIR DIPHOSPHATE GS-607596, MN2+ AND SYMMETRICAL PRIMER TEMPLATE 5'-CAAAAUUU


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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Ligand Structure Quality Assessment 


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:  
    4WT9, 4WTA, 4WTC, 4WTD, 4WTE, 4WTF, 4WTG, 4WTI, 4WTJ, 4WTK, 4WTL, 4WTM

  • 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 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 ...

    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: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymeraseC [auth A]572Hepatitis 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)
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 PRIMER TEMPLATE CAAAAUUUB [auth P], A [auth T]8synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    6GS (Subject of Investigation/LOI)
    Query on 6GS

    Download Ideal Coordinates CCD File 
    E [auth P]2'-deoxy-2'-fluoro-2'-methyluridine 5'-(trihydrogen diphosphate)
    C10 H15 F N2 O11 P2
    VPPLCOBQDZAMRD-VPCXQMTMSA-N
     Ligand Interaction
    MN
    Query on MN

    Download Ideal Coordinates CCD File 
    D [auth P], F [auth A], G [auth A]MANGANESE (II) ION
    Mn
    WAEMQWOKJMHJLA-UHFFFAOYSA-N
     Ligand Interaction
    CL
    Query on CL

    Download Ideal Coordinates CCD File 
    H [auth A]CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.90 Å
    • R-Value Free: 0.232 
    • R-Value Work: 0.179 
    • R-Value Observed: 0.181 
    • Space Group: P 65
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 140.44α = 90
    b = 140.44β = 90
    c = 91.62γ = 120
    Software Package:
    Software NamePurpose
    XSCALEdata scaling
    REFMACrefinement
    PDB_EXTRACTdata extraction
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Ligand Structure Quality Assessment  



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • 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