3U1J

Aprotinin bound to Dengue virus protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

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
  • Structures With Same Primary Citation

  • 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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine protease subunit NS2BA51Dengue virus 3 Singapore/8120/1995Mutation(s): 0 
EC: 3.4.21.91 (UniProt), 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)
Find proteins for Q5UB51 (Dengue virus type 3 (strain Singapore/8120/1995))
Explore Q5UB51 
Go to UniProtKB:  Q5UB51
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Serine protease NS3B191Dengue virus 3 Singapore/8120/1995Mutation(s): 0 
EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
Find proteins for Q5UB51 (Dengue virus type 3 (strain Singapore/8120/1995))
Explore Q5UB51 
Go to UniProtKB:  Q5UB51
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Pancreatic trypsin inhibitorE58Bos taurusMutation(s): 0 
Find proteins for P00974 (Bos taurus)
Explore P00974 
Go to UniProtKB:  P00974
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.789α = 90
b = 84.789β = 90
c = 66.031γ = 120
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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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
    Changes: Database references