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 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 2.1 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: https://doi.org/10.1038/nature18938
  • Primary Citation of Related Structures:  
    5LBS, 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. 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
envelope protein E
A, B
447Zika virusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013))
Explore A0A024B7W1 
Go to UniProtKB:  A0A024B7W1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A024B7W1
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8C [auth H],
D [auth I]		141Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8E [auth L],
F [auth M]		147Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
J [auth A],
K [auth B],
O [auth I]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO
Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
L [auth H]
M [auth H]
G [auth A],
H [auth A],
I [auth A],
L [auth H],
M [auth H],
N [auth I],
P [auth L],
Q [auth L],
R [auth L],
S [auth M],
T [auth M]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.799α = 90
b = 121.353β = 90
c = 257.855γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-07-13
    Changes: Derived calculations
  • Version 1.2: 2016-07-20
    Changes: Database references
  • Version 1.3: 2016-08-17
    Changes: Database references
  • Version 2.0: 2019-06-12
    Changes: Atomic model, Data collection, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description