5LBV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 2.0 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:  
    5LBS, 5LBV, 5LCV

  • 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-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 ...

    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

    Organizational Affiliation

    Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
envelope protein EA, B447Zika virusMutation(s): 0 
EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013))
Explore A0A024B7W1 
Go to UniProtKB:  A0A024B7W1
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseC5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42466VF
GlyCosmos:  G42466VF
GlyGen:  G42466VF
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.628α = 90
b = 213.566β = 90
c = 124.024γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-07-20
    Changes: Database references
  • Version 1.2: 2016-08-17
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary