9B82

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.38 Å
  • R-Value Free:  0.295 (Depositor), 0.294 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Plant-produced SARS-CoV-2 antibody engineered towards enhanced potency and in vivo efficacy.

de Taeye, S.W.Faye, L.Morel, B.Schriek, A.I.Umotoy, J.C.Yuan, M.Kuzmina, N.A.Turner, H.L.Zhu, X.Grunwald-Gruber, C.Poniman, M.Burger, J.A.Caniels, T.G.Fitchette, A.C.Desgagnes, R.Stordeur, V.Mirande, L.Beauverger, G.de Bree, G.Ozorowski, G.Ward, A.B.Wilson, I.A.Bukreyev, A.Sanders, R.W.Vezina, L.P.Beaumont, T.van Gils, M.J.Gomord, V.

(2025) Plant Biotechnol J 23: 4-16

  • DOI: https://doi.org/10.1111/pbi.14458
  • Primary Citation of Related Structures:  
    9ARU, 9B82

  • PubMed Abstract: 

    Prevention of severe COVID-19 disease by SARS-CoV-2 in high-risk patients, such as immuno-compromised individuals, can be achieved by administration of antibody prophylaxis, but producing antibodies can be costly. Plant expression platforms allow substantial lower production costs compared to traditional bio-manufacturing platforms depending on mammalian cells in bioreactors. In this study, we describe the expression, production and purification of the originally human COVA2-15 antibody in plants. Our plant-produced mAbs demonstrated comparable neutralizing activity with COVA2-15 produced in mammalian cells. Furthermore, they exhibited similar capacity to prevent SARS-CoV-2 infection in a hamster model. To further enhance these biosimilars, we performed three glyco- and protein engineering techniques. First, to increase antibody half-life, we introduced YTE-mutation in the Fc tail; second, optimization of N-linked glycosylation by the addition of a C-terminal ER-retention motif (HDEL), and finally; production of mAb in plant production lines lacking β-1,2-xylosyltransferase and α-1,3-fucosyltransferase activities (FX-KO). These engineered biosimilars exhibited optimized glycosylation, enhanced phagocytosis and NK cell activation capacity compared to conventional plant-produced S15 and M15 biosimilars, in some cases outperforming mammalian cell produced COVA2-15. These engineered antibodies hold great potential for enhancing in vivo efficacy of mAb treatment against COVID-19 and provide a platform for the development of antibodies against other emerging viruses in a cost-effective manner.


  • Organizational Affiliation

    Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1205Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
COVA2-15 antibody heavy chain232Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
COVA2-15 antibody light chain219Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.38 Å
  • R-Value Free:  0.295 (Depositor), 0.294 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.051α = 90
b = 218.66β = 112.34
c = 122.728γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesINV-004923

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release
  • Version 1.1: 2025-01-08
    Changes: Database references