4UTC

Crystal structure of dengue 2 virus envelope glycoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Recognition Determinants of Broadly Neutralizing Human Antibodies Against Dengue Viruses.

Rouvinski, A.Guardado-Calvo, P.Barba-Spaeth, G.Duquerroy, S.Vaney, M.Kikuti, C.M.Sanchez, M.E.N.Dejnirattisai, W.Wongwiwat, W.Haouz, A.Girard-Blanc, C.Petres, S.Shepard, W.E.Despres, P.Arenzana-Seisdedos, F.Dussart, P.Mongkolsapaya, J.Screaton, G.R.Rey, F.A.

(2015) Nature 520: 109

  • DOI: 10.1038/nature14130
  • Primary Citation of Related Structures:  
  • Also Cited By: 5N0A, 5N09, 5LBV, 5LBS

  • PubMed Abstract: 
  • Dengue disease is caused by four different flavivirus serotypes, which infect 390 million people yearly with 25% symptomatic cases and for which no licensed vaccine is available. Recent phase III vaccine trials showed partial protection, and in parti ...

    Dengue disease is caused by four different flavivirus serotypes, which infect 390 million people yearly with 25% symptomatic cases and for which no licensed vaccine is available. Recent phase III vaccine trials showed partial protection, and in particular no protection for dengue virus serotype 2 (refs 3, 4). Structural studies so far have characterized only epitopes recognized by serotype-specific human antibodies. We recently isolated human antibodies potently neutralizing all four dengue virus serotypes. Here we describe the X-ray structures of four of these broadly neutralizing antibodies in complex with the envelope glycoprotein E from dengue virus serotype 2, revealing that the recognition determinants are at a serotype-invariant site at the E-dimer interface, including the exposed main chain of the E fusion loop and the two conserved glycan chains. This 'E-dimer-dependent epitope' is also the binding site for the viral glycoprotein prM during virus maturation in the secretory pathway of the infected cell, explaining its conservation across serotypes and highlighting an Achilles' heel of the virus with respect to antibody neutralization. These findings will be instrumental for devising novel immunogens to protect simultaneously against all four serotypes of dengue virus.


    Related Citations: 
    • A New Class of Highly Potent, Broadly Neutralizing Antibodies Isolated from Viremic Patients Infected with Dengue Virus.
      Dejnirattisai, W.,Wongwiwat, W.,Supasa, S.,Zhang, X.,Dai, X.,Rouvinsky, A.,Jumnainsong, A.,Edwards, C.,Quyen, N.T.H.,Duangchinda, T.,Grimes, J.M.,Tsai, W.,Lai, C.,Wang, W.,Malasit, P.,Farrar, J.,Simmons, C.P.,Zhou, Z.H.,Rey, F.A.,Mongkolsapaya, J.,Screaton, G.R.
      (2015) Nat.Immunol. 16: 170


    Organizational Affiliation

    1] Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, 75724 Paris Cedex 15, France [2] CNRS UMR 3569 Virologie, 75724 Paris Cedex 15, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENVELOPE GLYCOPROTEIN E
A, B
422Dengue virus 2Mutation(s): 0 
Find proteins for A0A0B4SHY9 (Dengue virus 2)
Go to UniProtKB:  A0A0B4SHY9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

Download SDF File 
Download CCD File 
A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.211 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 105.462α = 90.00
b = 105.462β = 90.00
c = 165.895γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2015-04-08
    Type: Database references