5VIG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


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:  

  • 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 neutralizat ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab heavy chain
H, A
232N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab light chain
L, B
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Zika virus envelope protein DIII
Z, G
110Zika virusMutation(s): 0 
Find proteins for A0A192GPS0 (Zika virus)
Go to UniProtKB:  A0A192GPS0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download SDF File 
Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.212 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 385.082α = 90.00
b = 385.082β = 90.00
c = 56.640γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
PHASERphasing
Aimlessdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-05-17
    Type: Database references