2JLV

Dengue virus 4 NS3 helicase in complex with ssRNA and AMPPNP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

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.H., Xu, T., Watson, R.P., Becker, D.S., 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:  
    2JLS, 2JLR, 2JLQ, 2JLZ, 2JLY, 2JLX, 2JLW, 2JLV, 2JLU

  • 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 to single-stranded (ss) RNA, to an ATP analogue, to a transition-state analogue and to ATP hydrolysis products ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE PROTEASE SUBUNIT NS3A, B451Dengue virus 4 Thailand/0348/1991Mutation(s): 0 
EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q2YHF0 (Dengue virus type 4 (strain Thailand/0348/1991))
Explore Q2YHF0 
Go to UniProtKB:  Q2YHF0
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-R(*AP*GP*AP*CP*UP*AP*AP*CP*AP*AP*CP*U)-3'C, D12N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 4 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ANP
    Query on ANP
    Download Ideal Coordinates CCD File 
    		 E [auth A], I [auth B]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
    C10 H17 N6 O12 P3
    PVKSNHVPLWYQGJ-KQYNXXCUSA-N    		 Ligand Interaction
    GOL
    Query on GOL
    Download Ideal Coordinates CCD File 
    		 G [auth A], K [auth B]GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N    		 Ligand Interaction
    MN
    Query on MN
    Download Ideal Coordinates CCD File 
    		 F [auth A], J [auth B]MANGANESE (II) ION
    Mn
    WAEMQWOKJMHJLA-UHFFFAOYSA-N    		 Ligand Interaction
    CL
    Query on CL
    Download Ideal Coordinates CCD File 
    		 H [auth A], L [auth B]CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M    		 Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.90 Å
    • R-Value Free: 0.248 
    • R-Value Work: 0.190 
    • R-Value Observed: 0.193 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 132.66α = 90
    b = 105.192β = 117.66
    c = 72.435γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    MOSFLMdata reduction
    SCALAdata scaling

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

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