3KQL

Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal a Ratchet Translocation Mechanism


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.184 

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This is version 1.2 of the entry. See complete history


Literature

Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism.

Gu, M.Rice, C.M.

(2010) Proc Natl Acad Sci U S A 107: 521-528

  • DOI: 10.1073/pnas.0913380107
  • Primary Citation of Related Structures:  
    3KQH, 3KQK, 3KQL, 3KQN, 3KQU

  • PubMed Abstract: 
  • A virally encoded superfamily-2 (SF2) helicase (NS3h) is essential for the replication of hepatitis C virus, a leading cause of liver disease worldwide. Efforts to elucidate the function of NS3h and to develop inhibitors against it, however, have been hampered by limited understanding of its molecular mechanism ...

    A virally encoded superfamily-2 (SF2) helicase (NS3h) is essential for the replication of hepatitis C virus, a leading cause of liver disease worldwide. Efforts to elucidate the function of NS3h and to develop inhibitors against it, however, have been hampered by limited understanding of its molecular mechanism. Here we show x-ray crystal structures for a set of NS3h complexes, including ground-state and transition-state ternary complexes captured with ATP mimics (ADP.BeF(3) and ). These structures provide, for the first time, three conformational snapshots demonstrating the molecular basis of action for a SF2 helicase. Upon nucleotide binding, overall domain rotation along with structural transitions in motif V and the bound DNA leads to the release of one base from the substrate base-stacking row and the loss of several interactions between NS3h and the 3' DNA segment. As nucleotide hydrolysis proceeds into the transition state, stretching of a "spring" helix and another overall conformational change couples rearrangement of the (d)NTPase active site to additional hydrogen-bonding between NS3h and DNA. Together with biochemistry, these results demonstrate a "ratchet" mechanism involved in the unidirectional translocation and define the step size of NS3h as one base per nucleotide hydrolysis cycle. These findings suggest feasible strategies for developing specific inhibitors to block the action of this attractive, yet largely unexplored drug target.


    Organizational Affiliation

    Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY 10065, USA. mgu@rockefeller.edu



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine protease/NTPase/helicase NS3A, B437Hepatitis C virus (isolate Con1)Mutation(s): 0 
Gene Names: NS3
EC: 3.4.21.98 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.1 (PDB Primary Data), 3.4.22 (UniProt), 3.6.4.13 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q9WMX2 (Hepatitis C virus genotype 1b (isolate Con1))
Explore Q9WMX2 
Go to UniProtKB:  Q9WMX2
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*TP*TP*TP*TP*TP*T)-3'C [auth E], D [auth F]6N/A
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ADP (Subject of Investigation/LOI)
    Query on ADP

    Download Ideal Coordinates CCD File 
    F [auth A], I [auth B]ADENOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O10 P2
    XTWYTFMLZFPYCI-KQYNXXCUSA-N
     Ligand Interaction
    ALF
    Query on ALF

    Download Ideal Coordinates CCD File 
    E [auth A], H [auth B]TETRAFLUOROALUMINATE ION
    Al F4
    UYOMQIYKOOHAMK-UHFFFAOYSA-J
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    G [auth A], J [auth B]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.50 Å
    • R-Value Free: 0.211 
    • R-Value Work: 0.184 
    • Space Group: P 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 43.535α = 90
    b = 75.315β = 90.16
    c = 144.229γ = 90
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    PHASERphasing
    CNSrefinement
    PDB_EXTRACTdata extraction

    Structure Validation

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    Ligand Structure Quality Assessment  



    Entry History 

    Deposition Data

    • Deposited Date: 2009-11-17 
    • Released Date: 2010-01-26 
    • Deposition Author(s): Gu, M., Rice, C.M.

    Revision History  (Full details and data files)

    • Version 1.0: 2010-01-26
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance
    • Version 1.2: 2017-11-01
      Changes: Refinement description