6NIS

Crystal structure of a human anti-ZIKV-DENV neutralizing antibody MZ24 isolated following ZPIV vaccination


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report

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This is version 1.3 of the entry. See complete history


Literature

Potent Zika and dengue cross-neutralizing antibodies induced by Zika vaccination in a dengue-experienced donor.

Dussupt, V.Sankhala, R.S.Gromowski, G.D.Donofrio, G.De La Barrera, R.A.Larocca, R.A.Zaky, W.Mendez-Rivera, L.Choe, M.Davidson, E.McCracken, M.K.Brien, J.D.Abbink, P.Bai, H.Bryan, A.L.Bias, C.H.Berry, I.M.Botero, N.Cook, T.Doria-Rose, N.A.Escuer, A.G.I.Frimpong, J.A.Geretz, A.Hernandez, M.Hollidge, B.S.Jian, N.Kabra, K.Leggat, D.J.Liu, J.Pinto, A.K.Rutvisuttinunt, W.Setliff, I.Tran, U.Townsley, S.Doranz, B.J.Rolland, M.McDermott, A.B.Georgiev, I.S.Thomas, R.Robb, M.L.Eckels, K.H.Barranco, E.Koren, M.Smith, D.R.Jarman, R.G.George, S.L.Stephenson, K.E.Barouch, D.H.Modjarrad, K.Michael, N.L.Joyce, M.G.Krebs, S.J.

(2020) Nat Med 26: 228-235

  • DOI: https://doi.org/10.1038/s41591-019-0746-2
  • Primary Citation of Related Structures:  
    6MTX, 6MTY, 6NIP, 6NIS, 6NIU

  • PubMed Abstract: 

    Zika virus (ZIKV) has caused significant disease, with widespread cases of neurological pathology and congenital neurologic defects. Rapid vaccine development has led to a number of candidates capable of eliciting potent ZIKV-neutralizing antibodies (reviewed in refs. 1-3 ). Despite advances in vaccine development, it remains unclear how ZIKV vaccination affects immune responses in humans with prior flavivirus immunity. Here we show that a single-dose immunization of ZIKV purified inactivated vaccine (ZPIV) 4-7 in a dengue virus (DENV)-experienced human elicited potent cross-neutralizing antibodies to both ZIKV and DENV. Using a unique ZIKV virion-based sorting strategy, we isolated and characterized multiple antibodies, including one termed MZ4, which targets a novel site of vulnerability centered on the Envelope (E) domain I/III linker region and protects mice from viremia and viral dissemination following ZIKV or DENV-2 challenge. These data demonstrate that Zika vaccination in a DENV-experienced individual can boost pre-existing flavivirus immunity and elicit protective responses against both ZIKV and DENV. ZPIV vaccination in Puerto Rican individuals with prior flavivirus experience yielded similar cross-neutralizing potency after a single vaccination, highlighting the potential benefit of ZIKV vaccination in flavivirus-endemic areas.


  • Organizational Affiliation

    Emerging Infectious Diseases Branch, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MZ24 antibody heavy chainA [auth H]225Homo sapiensMutation(s): 0 
Gene Names: IGHV4-59*08
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MZ24 antibody light chainB [auth L]216Homo sapiensMutation(s): 0 
Gene Names: IGLV1-44*01
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth L],
H [auth L]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth H]
D [auth H]
E [auth H]
F [auth H]
I [auth L]
C [auth H],
D [auth H],
E [auth H],
F [auth H],
I [auth L],
J [auth L],
K [auth L],
L
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.85α = 90
b = 66.667β = 90
c = 134.416γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentUnited StatesW81XWH-07-2-0067

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2021-01-06
    Changes: Database references
  • Version 1.2: 2021-04-07
    Changes: Data collection
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description