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 8EEE

Crystal structure of a NHP anti-ZIKV neutralizing antibody rhMZ104-d in complex with ZIKV E glycoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Zika-specific neutralizing antibodies targeting inter-dimer envelope epitopes.

Sankhala, R.S.Dussupt, V.Donofrio, G.Gromowski, G.D.De La Barrera, R.A.Larocca, R.A.Mendez-Rivera, L.Lee, A.Choe, M.Zaky, W.Mantus, G.Jensen, J.L.Chen, W.H.Gohain, N.Bai, H.McCracken, M.K.Mason, R.D.Leggat, D.Slike, B.M.Tran, U.Jian, N.Abbink, P.Peterson, R.Mendes, E.A.Freitas de Oliveira Franca, R.Calvet, G.A.Bispo de Filippis, A.M.McDermott, A.Roederer, M.Hernandez, M.Albertus, A.Davidson, E.Doranz, B.J.Rolland, M.Robb, M.L.Lynch, R.M.Barouch, D.H.Jarman, R.G.Thomas, S.J.Modjarrad, K.Michael, N.L.Krebs, S.J.Joyce, M.G.

(2023) Cell Rep 42: 112942-112942

  • DOI: https://doi.org/10.1016/j.celrep.2023.112942
  • Primary Citation of Related Structures:  
    8EE5, 8EE8, 8EED, 8EEE, 8EEZ, 8EF0, 8EF1, 8EF2, 8EF3

  • PubMed Abstract: 

    Zika virus (ZIKV) is an emerging pathogen that causes devastating congenital defects. The overlapping epidemiology and immunologic cross-reactivity between ZIKV and dengue virus (DENV) pose complex challenges to vaccine design, given the potential for antibody-dependent enhancement of disease. Therefore, classification of ZIKV-specific antibody targets is of notable value. From a ZIKV-infected rhesus macaque, we identify ZIKV-reactive B cells and isolate potent neutralizing monoclonal antibodies (mAbs) with no cross-reactivity to DENV. We group these mAbs into four distinct antigenic groups targeting ZIKV-specific cross-protomer epitopes on the envelope glycoprotein. Co-crystal structures of representative mAbs in complex with ZIKV envelope glycoprotein reveal envelope-dimer epitope and unique dimer-dimer epitope targeting. All four specificities are serologically identified in convalescent humans following ZIKV infection, and representative mAbs from all four groups protect against ZIKV replication in mice. These results provide key insights into ZIKV-specific antigenicity and have implications for ZIKV vaccine, diagnostic, and therapeutic development.


  • Organizational Affiliation

    Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope protein EA [auth Z],
B [auth E]
405Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013Mutation(s): 0 
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 AnnotationsExpand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
rhMZ104-D antibody light chainC [auth L],
F [auth B]
220Macaca mulattaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence AnnotationsExpand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
rhMZ104-D antibody heavy chainD [auth H],
E [auth A]
228Macaca mulattaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence AnnotationsExpand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.32α = 90
b = 130.42β = 104.17
c = 109.71γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Defense (DOD, United States)United StatesW81XWH-07-2-0067

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Structure summary