3U1J

Aprotinin bound to Dengue virus protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Ligand-bound structures of the dengue virus protease reveal the active conformation

Noble, C.G.Seh, C.C.Chao, A.T.Shi, P.Y.

(2012) J.Virol. 86: 438-446

  • DOI: 10.1128/JVI.06225-11
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dengue is a mosquito-borne viral hemorrhagic disease that is a major threat to human health in tropical and subtropical regions. Here we report crystal structures of a peptide covalently bound to dengue virus serotype 3 (DENV-3) protease as well as t ...

    Dengue is a mosquito-borne viral hemorrhagic disease that is a major threat to human health in tropical and subtropical regions. Here we report crystal structures of a peptide covalently bound to dengue virus serotype 3 (DENV-3) protease as well as the serine-protease inhibitor aprotinin bound to the same enzyme. These structures reveal, for the first time, a catalytically active, closed conformation of the DENV protease. In the presence of the peptide, the DENV-3 protease forms the closed conformation in which the hydrophilic β-hairpin region of NS2B wraps around the NS3 protease core, in a manner analogous to the structure of West Nile virus (WNV) protease. Our results confirm that flavivirus proteases form the closed conformation during proteolysis, as previously proposed for WNV. The current DENV-3 protease structures reveal the detailed interactions at the P4' to P3 sites of the substrate. The new structural information explains the sequence preference, particularly for long basic residues in the nonprime side, as well as the difference in substrate specificity between the WNV and DENV proteases at the prime side. Structural analysis of the DENV-3 protease-peptide complex revealed a pocket that is formed by residues from NS2B and NS3; this pocket also exists in the WNV NS2B/NS3 protease structure and could be targeted for potential antivirus development. The structural information presented in the current study is invaluable for the design of specific inhibitors of DENV protease.


    Organizational Affiliation

    Novartis Institute for Tropical Diseases, Chromos, Singapore. christian.noble@novartis.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine protease subunit NS2B
A
51Dengue virus type 3 (strain Singapore/8120/1995)Mutation(s): 0 
Find proteins for Q5UB51 (Dengue virus type 3 (strain Singapore/8120/1995))
Go to UniProtKB:  Q5UB51
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Serine protease NS3
B
191Dengue virus type 3 (strain Singapore/8120/1995)Mutation(s): 0 
Find proteins for Q5UB51 (Dengue virus type 3 (strain Singapore/8120/1995))
Go to UniProtKB:  Q5UB51
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Pancreatic trypsin inhibitor
E
58Bos taurusMutation(s): 0 
Find proteins for P00974 (Bos taurus)
Go to UniProtKB:  P00974
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.186 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 84.789α = 90.00
b = 84.789β = 90.00
c = 66.031γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-09-30 
  • Released Date: 2011-11-09 
  • Deposition Author(s): Noble, C.G.

Revision History 

  • Version 1.0: 2011-11-09
    Type: Initial release
  • Version 1.1: 2013-06-05
    Type: Database references