RCSB PDB - 9ARU: COVA2-15 fragment antigen binding in complex with SARS-CoV-2 6P-mut7 S protein

 9ARU

COVA2-15 fragment antigen binding in complex with SARS-CoV-2 6P-mut7 S protein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoproteinA,
D [auth B],
G [auth C]
1,280Severe acute respiratory syndrome coronavirus 2Mutation(s): 11 
Gene Names: S2
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: 15Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
COVA2-15 heavy chain variable regionB [auth H],
E [auth D],
H [auth E]
129Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
COVA2-15 kappa chain variable regionC [auth L],
F,
I [auth G]
112Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth C]
BA [auth A]
BB [auth C]
CA [auth A]
DA [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01 AI110657

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release