7A3O

Crystal structure of dengue 1 virus envelope glycoprotein in complex with the scFv fragment of the broadly neutralizing human antibody EDE1 C10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The epitope arrangement on flavivirus particles contributes to Mab C10's extraordinary neutralization breadth across Zika and dengue viruses.

Sharma, A.Zhang, X.Dejnirattisai, W.Dai, X.Gong, D.Wongwiwat, W.Duquerroy, S.Rouvinski, A.Vaney, M.C.Guardado-Calvo, P.Haouz, A.England, P.Sun, R.Zhou, Z.H.Mongkolsapaya, J.Screaton, G.R.Rey, F.A.

(2021) Cell 184: 6052-6066.e18

  • DOI: https://doi.org/10.1016/j.cell.2021.11.010
  • Primary Citation of Related Structures:  
    7A3N, 7A3O, 7A3P, 7A3Q, 7A3R, 7A3S, 7A3T, 7A3U, 7CTH

  • PubMed Abstract: 

    The human monoclonal antibody C10 exhibits extraordinary cross-reactivity, potently neutralizing Zika virus (ZIKV) and the four serotypes of dengue virus (DENV1-DENV4). Here we describe a comparative structure-function analysis of C10 bound to the envelope (E) protein dimers of the five viruses it neutralizes. We demonstrate that the C10 Fab has high affinity for ZIKV and DENV1 but not for DENV2, DENV3, and DENV4. We further show that the C10 interaction with the latter viruses requires an E protein conformational landscape that limits binding to only one of the three independent epitopes per virion. This limited affinity is nevertheless counterbalanced by the particle's icosahedral organization, which allows two different dimers to be reached by both Fab arms of a C10 immunoglobulin. The epitopes' geometric distribution thus confers C10 its exceptional neutralization breadth. Our results highlight the importance not only of paratope/epitope complementarity but also the topological distribution for epitope-focused vaccine design.


  • Organizational Affiliation

    Institut Pasteur, Université de Paris, CNRS UMR3569, Unité de Virologie Structurale, 75015 Paris, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Core protein432dengue virus type 1Mutation(s): 0 
EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
Find proteins for Q9II02 (dengue virus type 1)
Explore Q9II02 
Go to UniProtKB:  Q9II02
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9II02
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Single chain variable fragment (scFv) from antibody EDE1 C10B [auth H]144Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Single chain variable fragment (scFv) from antibody EDE1 C10C [auth L]154Homo sapiensMutation(s): 0 
Entity Groups  
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth B]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.555α = 90
b = 135.555β = 90
c = 160.268γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHENIXphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-08
    Type: Initial release
  • Version 1.1: 2021-12-15
    Changes: Database references, Derived calculations
  • Version 1.2: 2021-12-22
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description