3KQU

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Inaugural Article: 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
  • Structures With Same Primary Citation

  • 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 bee ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine protease/NTPase/helicase NS3
A, B, C, D, E, F
437Hepatitis 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)
Find proteins for Q9WMX2 (Hepatitis C virus genotype 1b (isolate Con1))
Go to UniProtKB:  Q9WMX2
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*T*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'M, N19N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A, B, C, D, E, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
BEF
Query on BEF

Download CCD File 
A, B, C, D, E, F
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
MN
Query on MN

Download CCD File 
A, B, C, D, E, F
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.197 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.534α = 90
b = 116.467β = 90
c = 71.114γ = 119.97
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History 

  • 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