8DV6 | pdb_00008dv6

Zika virus envelope protein structure in complex with a potent Human mAb


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.38 Å
  • R-Value Free: 
    0.259 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8DV6

This is version 1.3 of the entry. See complete history

Literature

Structure and neutralization mechanism of a human antibody targeting a complex Epitope on Zika virus.

Adams, C.Carbaugh, D.L.Shu, B.Ng, T.S.Castillo, I.N.Bhowmik, R.Segovia-Chumbez, B.Puhl, A.C.Graham, S.Diehl, S.A.Lazear, H.M.Lok, S.M.de Silva, A.M.Premkumar, L.

(2023) PLoS Pathog 19: e1010814-e1010814

  • DOI: https://doi.org/10.1371/journal.ppat.1010814
  • Primary Citation Related Structures: 
    7YAR, 8DV6

  • PubMed Abstract: 

    We currently have an incomplete understanding of why only a fraction of human antibodies that bind to flaviviruses block infection of cells. Here we define the footprint of a strongly neutralizing human monoclonal antibody (mAb G9E) with Zika virus (ZIKV) by both X-ray crystallography and cryo-electron microscopy. Flavivirus envelope (E) glycoproteins are present as homodimers on the virion surface, and G9E bound to a quaternary structure epitope spanning both E protomers forming a homodimer. As G9E mainly neutralized ZIKV by blocking a step after viral attachment to cells, we tested if the neutralization mechanism of G9E was dependent on the mAb cross-linking E molecules and blocking low-pH triggered conformational changes required for viral membrane fusion. We introduced targeted mutations to the G9E paratope to create recombinant antibodies that bound to the ZIKV envelope without cross-linking E protomers. The G9E paratope mutants that bound to a restricted epitope on one protomer poorly neutralized ZIKV compared to the wild-type mAb, demonstrating that the neutralization mechanism depended on the ability of G9E to cross-link E proteins. In cell-free low pH triggered viral fusion assay, both wild-type G9E, and epitope restricted paratope mutant G9E bound to ZIKV but only the wild-type G9E blocked fusion. We propose that, beyond antibody binding strength, the ability of human antibodies to cross-link E-proteins is a critical determinant of flavivirus neutralization potency.


  • Organizational Affiliation
    • Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America.

Macromolecule Content 

  • Total Structure Weight: 188.46 kDa 
  • Atom Count: 12,838 
  • Modeled Residue Count: 1,695 
  • Deposited Residue Count: 1,742 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope protein E
A, B
415Zika virus ZIKV/Human/Cambodia/FSS13025/2010Mutation(s): 0 
UniProt
Find proteins for A0A173AEF6 (Zika virus)
Explore A0A173AEF6 
Go to UniProtKB:  A0A173AEF6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A173AEF6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
mAb Fab Heavy ChainC,
E [auth H]
240Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
mAb Fab Light ChainD,
F [auth L]
216Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.38 Å
  • R-Value Free:  0.259 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.041α = 90
b = 133.609β = 106.494
c = 105.109γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesBAA 2017-N-18041

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-04
    Type: Initial release
  • Version 1.1: 2023-07-19
    Changes: Database references, Refinement description
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary