5LBV

Structural basis of zika and dengue virus potent antibody cross-neutralization


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of potent Zika-dengue virus antibody cross-neutralization.

Barba-Spaeth, G.Dejnirattisai, W.Rouvinski, A.Vaney, M.C.Medits, I.Sharma, A.Simon-Loriere, E.Sakuntabhai, A.Cao-Lormeau, V.M.Haouz, A.England, P.Stiasny, K.Mongkolsapaya, J.Heinz, F.X.Screaton, G.R.Rey, F.A.

(2016) Nature 536: 48-53

  • DOI: 10.1038/nature18938
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Zika virus is a member of the Flavivirus genus that had not been associated with severe disease in humans until the recent outbreaks, when it was linked to microcephaly in newborns in Brazil and to Guillain-BarrĂ© syndrome in adults in French Polynesi ...

    Zika virus is a member of the Flavivirus genus that had not been associated with severe disease in humans until the recent outbreaks, when it was linked to microcephaly in newborns in Brazil and to Guillain-Barré syndrome in adults in French Polynesia. Zika virus is related to dengue virus, and here we report that a subset of antibodies targeting a conformational epitope isolated from patients with dengue virus also potently neutralize Zika virus. The crystal structure of two of these antibodies in complex with the envelope protein of Zika virus reveals the details of a conserved epitope, which is also the site of interaction of the envelope protein dimer with the precursor membrane (prM) protein during virus maturation. Comparison of the Zika and dengue virus immunocomplexes provides a lead for rational, epitope-focused design of a universal vaccine capable of eliciting potent cross-neutralizing antibodies to protect simultaneously against both Zika and dengue virus infections.


    Related Citations: 
    • Recognition determinants of broadly neutralizing human antibodies against dengue viruses.
      Rouvinski, A.,Guardado-Calvo, P.,Barba-Spaeth, G.,Duquerroy, S.,Vaney, M.C.,Kikuti, C.M.,Navarro Sanchez, M.E.,Dejnirattisai, W.,Wongwiwat, W.,Haouz, A.,Girard-Blanc, C.,Petres, S.,Shepard, W.E.,Despres, P.,Arenzana-Seisdedos, F.,Dussart, P.,Mongkolsapaya, J.,Screaton, G.R.,Rey, F.A.
      (2015) Nature 520: 109
    • A new class of highly potent, broadly neutralizing antibodies isolated from viremic patients infected with dengue virus.
      Dejnirattisai, W.,Wongwiwat, W.,Supasa, S.,Zhang, X.,Dai, X.,Rouvinski, A.,Rouvinsky, A.,Jumnainsong, A.,Edwards, C.,Quyen, N.T.,Duangchinda, T.,Grimes, J.M.,Tsai, W.Y.,Lai, C.Y.,Wang, W.K.,Malasit, P.,Farrar, J.,Simmons, C.P.,Zhou, Z.H.,Rey, F.A.,Mongkolsapaya, J.,Screaton, G.R.
      (2015) Nat. Immunol. 16: 170



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
envelope protein E
A, B
447Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)Mutation(s): 0 
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013))
Go to UniProtKB:  A0A024B7W1
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.207 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 64.628α = 90.00
b = 213.566β = 90.00
c = 124.024γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-06-17 
  • Released Date: 2016-07-06 
  • Deposition Author(s): Barba-Spaeth, G.

Revision History 

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-07-20
    Type: Database references
  • Version 1.2: 2016-08-17
    Type: Database references