5VIG

Crystal structure of anti-Zika antibody Z006 bound to Zika virus envelope protein DIII


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Recurrent Potent Human Neutralizing Antibodies to Zika Virus in Brazil and Mexico.

Robbiani, D.F.Bozzacco, L.Keeffe, J.R.Khouri, R.Olsen, P.C.Gazumyan, A.Schaefer-Babajew, D.Avila-Rios, S.Nogueira, L.Patel, R.Azzopardi, S.A.Uhl, L.F.K.Saeed, M.Sevilla-Reyes, E.E.Agudelo, M.Yao, K.H.Golijanin, J.Gristick, H.B.Lee, Y.E.Hurley, A.Caskey, M.Pai, J.Oliveira, T.Wunder, E.A.Sacramento, G.Nery, N.Orge, C.Costa, F.Reis, M.G.Thomas, N.M.Eisenreich, T.Weinberger, D.M.de Almeida, A.R.P.West, A.P.Rice, C.M.Bjorkman, P.J.Reyes-Teran, G.Ko, A.I.MacDonald, M.R.Nussenzweig, M.C.

(2017) Cell 169: 597-609.e11

  • DOI: https://doi.org/10.1016/j.cell.2017.04.024
  • Primary Citation of Related Structures:  
    5VIC, 5VIG

  • PubMed Abstract: 

    Antibodies to Zika virus (ZIKV) can be protective. To examine the antibody response in individuals who develop high titers of anti-ZIKV antibodies, we screened cohorts in Brazil and Mexico for ZIKV envelope domain III (ZEDIII) binding and neutralization. We find that serologic reactivity to dengue 1 virus (DENV1) EDIII before ZIKV exposure is associated with increased ZIKV neutralizing titers after exposure. Antibody cloning shows that donors with high ZIKV neutralizing antibody titers have expanded clones of memory B cells that express the same immunoglobulin VH3-23/VK1-5 genes. These recurring antibodies cross-react with DENV1, but not other flaviviruses, neutralize both DENV1 and ZIKV, and protect mice against ZIKV challenge. Structural analyses reveal the mechanism of recognition of the ZEDIII lateral ridge by VH3-23/VK1-5 antibodies. Serologic testing shows that antibodies to this region correlate with serum neutralizing activity to ZIKV. Thus, high neutralizing responses to ZIKV are associated with pre-existing reactivity to DENV1 in humans.


  • Organizational Affiliation

    Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA. Electronic address: drobbiani@rockefeller.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab heavy chainA [auth H],
D [auth A]
232Homo sapiensMutation(s): 0 
UniProt
Find proteins for S6B291 (Homo sapiens)
Explore S6B291 
Go to UniProtKB:  S6B291
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS6B291
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab light chainB [auth L],
E [auth B]
213Homo sapiensMutation(s): 0 
UniProt
Find proteins for P0DOX7 (Homo sapiens)
Explore P0DOX7 
Go to UniProtKB:  P0DOX7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DOX7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Zika virus envelope protein DIIIC [auth Z],
F [auth G]
110Zika virusMutation(s): 0 
UniProt
Find proteins for A0A192GPS0 (Zika virus)
Explore A0A192GPS0 
Go to UniProtKB:  A0A192GPS0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A192GPS0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download Ideal Coordinates CCD File 
G [auth A]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 385.082α = 90
b = 385.082β = 90
c = 56.64γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-05-17
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Structure summary