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TitleCryo-EM reveals conformational variability in the SARS-CoV-2 spike protein RBD induced by two broadly neutralizing monoclonal antibodies.
Journal, issue, pagesRSC Adv, Vol. 15, Issue 18, Page 14385-14399, Year 2025
Publish dateApr 28, 2025
AuthorsClayton Fernando Rencilin / Arnab Chatterjee / Mohammad Yousuf Ansari / Suprit Deshpande / Sohini Mukherjee / Randhir Singh / Sowrabha B Jayatheertha / Poorvi M Reddy / Nitin Hingankar / Raghavan Varadarajan / Jayanta Bhattacharya / Somnath Dutta /
PubMed AbstractSARS-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 ...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.
External linksRSC Adv / PubMed:40330036 / PubMed Central
MethodsEM (single particle)
Resolution4.4 - 7.3 Å
Structure data

34546

8ybs

EMDB-34546, PDB-8ybs:
State - I: Spike 2-up RBD with THSC20.HVTR04 (Fab4)
Method: EM (single particle) / Resolution: 4.54 Å

EMDB-34547: Spike 3-up RBD with THSC20.HVTR04 (Fab4): State - II
Method: EM (single particle) / Resolution: 5.152 Å

EMDB-34548: Spike 3-up RBD with THSC20.HVTR04 (Fab4): State - III
Method: EM (single particle) / Resolution: 4.9 Å

34563

8yby

EMDB-34563: Spike 2-up RBD with THSC20.HVTR26 (Fab26): State - I
PDB-8yby: State - I: Spike 2-up RBD with THSC20.HVTR26 (Fab26) - single Fab masked
Method: EM (single particle) / Resolution: 4.4 Å

EMDB-34602: State - I: Spike 2-up RBD with THSC20.HVTR26 (Fab26)
Method: EM (single particle) / Resolution: 7.3 Å

34603

8ybz

EMDB-34603, PDB-8ybz:
State - II: Spike 3-up RBD with THSC20.HVTR26 (Fab26)
Method: EM (single particle) / Resolution: 4.8 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

Source
  • Severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
  • severe acute respiratory syndrome coronavirus
KeywordsPROTEIN BINDING / Cryo-EM Analysis / Spike Protein / monoclonal antibody

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