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 8KDS

Trimer state of SARS-CoV Spike protein complexed with antibody PW5-535


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 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

Potent and broadly neutralizing antibodies against sarbecoviruses induced by sequential COVID-19 vaccination.

Zhao, X.Qiu, T.Huang, X.Mao, Q.Wang, Y.Qiao, R.Li, J.Mao, T.Wang, Y.Cun, Y.Wang, C.Luo, C.Yoon, C.Wang, X.Li, C.Cui, Y.Zhao, C.Li, M.Chen, Y.Cai, G.Geng, W.Hu, Z.Cao, J.Zhang, W.Cao, Z.Chu, H.Sun, L.Wang, P.

(2024) Cell Discov 10: 14-14

  • DOI: https://doi.org/10.1038/s41421-024-00648-1
  • Primary Citation of Related Structures:  
    8KDM, 8KDR, 8KDS, 8KDT, 8KEH, 8KEJ, 8KEK, 8KEO, 8KEP, 8KEQ, 8KER

  • PubMed Abstract: 

    The current SARS-CoV-2 variants strikingly evade all authorized monoclonal antibodies and threaten the efficacy of serum-neutralizing activity elicited by vaccination or prior infection, urging the need to develop antivirals against SARS-CoV-2 and related sarbecoviruses. Here, we identified both potent and broadly neutralizing antibodies from a five-dose vaccinated donor who exhibited cross-reactive serum-neutralizing activity against diverse coronaviruses. Through single B-cell sorting and sequencing followed by a tailor-made computational pipeline, we successfully selected 86 antibodies with potential cross-neutralizing ability from 684 antibody sequences. Among them, PW5-570 potently neutralized all SARS-CoV-2 variants that arose prior to Omicron BA.5, and the other three could broadly neutralize all current SARS-CoV-2 variants of concern, SARS-CoV and their related sarbecoviruses (Pangolin-GD, RaTG13, WIV-1, and SHC014). Cryo-EM analysis demonstrates that these antibodies have diverse neutralization mechanisms, such as disassembling spike trimers, or binding to RBM or SD1 to affect ACE2 binding. In addition, prophylactic administration of these antibodies significantly protects nasal turbinate and lung infections against BA.1, XBB.1, and SARS-CoV viral challenge in golden Syrian hamsters, respectively. Importantly, post-exposure treatment with PW5-5 and PW5-535 also markedly protects against XBB.1 challenge in these models. This study reveals the potential utility of computational process to assist screening cross-reactive antibodies, as well as the potency of vaccine-induced broadly neutralizing antibodies against current SARS-CoV-2 variants and related sarbecoviruses, offering promising avenues for the development of broad therapeutic antibody drugs.


  • Organizational Affiliation

    Shanghai Pudong Hospital, Fudan University Pudong Medical Center, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Institutes of Biomedical Sciences, Shanghai Sci-Tech Inno Center for Infection & Immunity, Fudan University, Shanghai, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PW5-535 heavy chainA [auth E],
C [auth G],
E [auth I]
450Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence AnnotationsExpand
  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PW5-535 light chainB [auth D],
D [auth F],
F [auth H]
215Homo sapiensMutation(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
Spike glycoproteinG [auth B],
H [auth A],
I [auth C]
1,190Severe acute respiratory syndrome coronavirus 2Mutation(s): 3 
UniProt
Find proteins for P59594 (Severe acute respiratory syndrome coronavirus)
Explore P59594 
Go to UniProtKB:  P59594
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59594
Sequence AnnotationsExpand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81900729

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-14
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Structure summary