9NQZ | pdb_00009nqz

cryo-EM structure of broad betacoronavirus binding antibody 1871 in complex with OC43 S2 subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Human antibody targeting of coronavirus spike S2 subunit is associated with protection mediated by Fc effector functions.

Muthuraman, K.Jackman, M.Liang, Y.Garrett, M.E.Cui, H.Nguyen, L.V.H.Ivanochko, D.Ye, C.Pino, P.A.Hicks, A.Maingot, B.Yusko, E.Benzeno, S.Martinez-Sobrido, L.Torrelles, J.B.Gilbert, A.E.Rubin, B.E.R.Keitany, G.Jetha, A.Julien, J.-P.

(2025) J Virol : e0152325-e0152325

  • DOI: https://doi.org/10.1128/jvi.01523-25
  • Primary Citation of Related Structures:  
    9NQZ

  • PubMed Abstract: 

    Over the past two decades, betacoronaviruses (β-CoVs) have caused two epidemics and a pandemic and remain a high risk for future outbreaks through zoonotic transmissions, highlighting the need for broad biomedical countermeasures. Here, we describe a convalescent human monoclonal antibody (mAb 1871) that targets the S2 subunit of the coronavirus spike protein, with broad β-CoVs binding and sarbecovirus neutralization. Cryo-electron microscopy analysis revealed that mAb 1871 binds the upstream helix of the S2 subunit, interacting with partially conserved residues, providing a molecular basis for its cross-reactivity. Though less potent than receptor-binding domain-directed antibodies-approximately 500-fold lower neutralization potency than the emergency use authorized receptor-binding domain (RBD)-directed Pemgarda mAb against wild-type SARS-CoV-2-mAb 1871 provides protective efficacy in a mouse model. Notably, Fc effector functions are critical for its in vivo protection. This study further highlights the Fc dependence of S2-directed antibodies for in vivo protection and identifies a conserved epitope in the S2 subunit as a potential target of broad-β-CoVs countermeasures.IMPORTANCEBats and pangolins are natural reservoirs of betacoronaviruses (β-CoVs) and continue to pose a significant risk for future outbreaks through zoonotic transmissions. This highlights the need for effective countermeasures to prevent future pandemics. While neutralizing antibodies targeting the receptor-binding domain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) received emergency use authorization, many have lost efficacy as the virus evolved, and authorizations have been revoked. In contrast to the S1 subunit, the spike protein S2 subunit is more conserved across β-CoVs, making it an attractive target for the development of broadly neutralizing antibodies. Here, we describe a human mAb that targets a conserved epitope in the S2 subunit, demonstrating broad β-CoV binding, sarbecovirus neutralization, and in vivo protection mediated by Fc effector functions in a mouse model. These findings have important implications for pan-β-CoVs therapeutics and vaccine development.


  • Organizational Affiliation
    • Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
585Human coronavirus OC43Mutation(s): 0 
UniProt
Find proteins for A0A0B4N716 (Human coronavirus OC43)
Explore A0A0B4N716 
Go to UniProtKB:  A0A0B4N716
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B4N716
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
1871 Fab light chainD,
F,
I [auth L]
109Homo sapiensMutation(s): 0 
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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
1871 Fab heavy chain
E, G, H
125Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_5127

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesINV-023398

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release
  • Version 1.1: 2025-12-03
    Changes: Data collection, Database references