5VIC

Crystal structure of anti-Zika antibody Z004 bound to DENV-1 Envelope protein DIII


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

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This is version 1.1 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: 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 ...

    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; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA. Electronic address: nussen@rockefeller.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fab heavy chainA [auth H]234Homo sapiensMutation(s): 0 
UniProt
Find proteins for S6B291 (Homo sapiens)
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Go to UniProtKB:  S6B291
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab light chainB [auth L]214Homo sapiensMutation(s): 0 
UniProt
Find proteins for P0DOX7 (Homo sapiens)
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Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Dengue 1 Envelope DIII domainC [auth E]99Dengue virus 1 Nauru/West Pac/1974Mutation(s): 0 
UniProt
Find proteins for Q8BE39 (Dengue virus 1)
Explore Q8BE39 
Go to UniProtKB:  Q8BE39
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.225α = 90
b = 74.225β = 90
c = 190.758γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

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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