8YBY | pdb_00008yby

State - I: Spike 2-up RBD with THSC20.HVTR26 (Fab26) - single Fab masked


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 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

Cryo-EM reveals conformational variability in the SARS-CoV-2 spike protein RBD induced by two broadly neutralizing monoclonal antibodies.

Rencilin, C.F.Chatterjee, A.Ansari, M.Y.Deshpande, S.Mukherjee, S.Singh, R.Jayatheertha, S.B.Reddy, P.M.Hingankar, N.Varadarajan, R.Bhattacharya, J.Dutta, S.

(2025) RSC Adv 15: 14385-14399

  • DOI: https://doi.org/10.1039/d5ra00373c
  • Primary Citation of Related Structures:  
    8YBS, 8YBY, 8YBZ

  • PubMed Abstract: 

    SARS-CoV-2 spike proteins play a critical role in infection by interacting with the ACE2 receptors. Their receptor-binding domains and N-terminal domains exhibit remarkable flexibility and can adopt various conformations that facilitate receptor engagement. Previous structural studies have reported the RBD of the spike protein in "up", "down", and various intermediate states, as well as its different conformational changes during ACE2 binding. This flexibility also influences its interactions with the neutralizing antibodies, yet its role in the antibody complexes remains understudied. In this study, we used cryo-electron microscopy to investigate the structural properties of two broadly neutralizing monoclonal antibodies, THSC20.HVTR04 and THSC20.HVTR26. These antibodies were isolated from an unvaccinated individual and demonstrated potent neutralization of multiple SARS-CoV-2 variants. Our analysis revealed distinct binding characteristics and conformational changes in the spike RBD upon binding with the monoclonal antibodies. The structural characterization of the spike protein-monoclonal antibody complexes provided valuable insights into the structural variability of the spike protein and the possible mechanisms for antibody-mediated neutralization.


  • Organizational Affiliation
    • Molecular Biophysics Unit, Indian Institute of Science Bengaluru 560012 India somnath@iisc.ac.in.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoproteinA [auth B],
D,
E
1,273Severe acute respiratory syndrome coronavirusMutation(s): 0 
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
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
THSC20.HVTR26 (Fab26) - Heavy ChainB [auth A]231Homo 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
THSC20.HVTR26 (Fab26) - Light Chain216Homo 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: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaBT/INF/22/SP22844/2017
Department of Biotechnology (DBT, India)IndiaSR/FST/LSII-039/2015
Science and Engineering Research Board (SERB)IndiaSERB-EMR/2016/000608and SERB-IPA/2020/000094
Bill & Melinda Gates FoundationUnited StatesINV-030592
Department of Biotechnology (DBT, India)IndiaIA/TSG/19/1/600019

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-19
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Database references