4UTA

Crystal structure of dengue 2 virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE1 C8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 2.1 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: https://doi.org/10.1038/nature14130
  • Primary Citation of Related Structures:  
    4UT6, 4UT7, 4UT9, 4UTA, 4UTB, 4UTC

  • 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 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.


  • 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ENVELOPE GLYCOPROTEIN E
A, B
425dengue virus type 2Mutation(s): 0 
UniProt
Find proteins for A0A0B4SHY9 (dengue virus type 2)
Explore A0A0B4SHY9 
Go to UniProtKB:  A0A0B4SHY9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B4SHY9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8 HEAVY CHAINC [auth H],
D [auth I]
272Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8 LIGHT CHAINE [auth L],
F [auth M]
217Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth C]4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH
GlyCosmos:  G32152BH
GlyGen:  G32152BH
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth D]6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G82348BZ
GlyCosmos:  G82348BZ
GlyGen:  G82348BZ
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.657α = 90
b = 191.342β = 90
c = 203.663γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2015-04-08
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary