5LBS

structural basis of Zika and Dengue virus potent antibody cross-neutralization


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 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 virusMutation(s): 0 
Find proteins for A0A024B7W1 (Zika virus)
Go to UniProtKB:  A0A024B7W1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8
H, I
141N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8
L, M
147N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, I
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, H, I, L, M
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.194 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 60.799α = 90.00
b = 121.353β = 90.00
c = 257.855γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
Aimlessdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-07-13
    Type: Derived calculations
  • Version 1.2: 2016-07-20
    Type: Database references
  • Version 1.3: 2016-08-17
    Type: Database references