2JLU

Dengue virus 4 NS3 helicase in complex with ssRNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Insights Into RNA Unwinding and ATP Hydrolysis by the Flavivirus Ns3 Protein.

Luo, D., Xu, T., Watson, R.P., Scherer-Becker, D., Sampath, A., Jahnke, W., Yeong, S.S., Wang, C.H., Lim, S.P., Strongin, A., Vasudevan, S.G., Lescar, J.

(2008) Embo J. 27: 3209

  • DOI: 10.1038/emboj.2008.232
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Together with the NS5 polymerase, the NS3 helicase has a pivotal function in flavivirus RNA replication and constitutes an important drug target. We captured the dengue virus NS3 helicase at several stages along the catalytic pathway including bound ...

    Together with the NS5 polymerase, the NS3 helicase has a pivotal function in flavivirus RNA replication and constitutes an important drug target. We captured the dengue virus NS3 helicase at several stages along the catalytic pathway including bound to single-stranded (ss) RNA, to an ATP analogue, to a transition-state analogue and to ATP hydrolysis products. RNA recognition appears largely sequence independent in a way remarkably similar to eukaryotic DEAD box proteins Vasa and eIF4AIII. On ssRNA binding, the NS3 enzyme switches to a catalytic-competent state imparted by an inward movement of the P-loop, interdomain closure and a change in the divalent metal coordination shell, providing a structural basis for RNA-stimulated ATP hydrolysis. These structures demonstrate for the first time large quaternary changes in the flaviviridae helicase, identify the catalytic water molecule and point to a beta-hairpin that protrudes from subdomain 2, as a critical element for dsRNA unwinding. They also suggest how NS3 could exert an effect as an RNA-anchoring device and thus participate both in flavivirus RNA replication and assembly.

    Organizational Affiliation: 

    Structural & Computational Biology Division, School of Biological Sciences, Nanyang Technological University, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERINE PROTEASE SUBUNIT NS3
A, B
451Dengue virus type 4 (strain Thailand/0348/1991)Mutation(s): 0 
Find proteins for Q2YHF0 (Dengue virus type 4 (strain Thailand/0348/1991))
Go to UniProtKB:  Q2YHF0
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*AP*GP*AP*CP*UP*AP*AP*CP*AP*AP*CP*U)-3'C,D12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 132.033α = 90.00
b = 105.497β = 117.54
c = 72.517γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance