8YBZ image
Deposition Date 2024-02-16
Release Date 2025-02-19
Last Version Date 2025-09-10
Entry Detail
PDB ID:
8YBZ
Keywords:
Title:
State - II: Spike 3-up RBD with THSC20.HVTR26 (Fab26)
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
4.80 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Spike glycoprotein
Gene (Uniprot):S
Chain IDs:A, B, C
Chain Length:1273
Number of Molecules:3
Biological Source:Severe acute respiratory syndrome coronavirus
Polymer Type:polypeptide(L)
Molecule:THSC20.HVTR26 (Fab26) - Heavy Chain
Chain IDs:D (auth: F), F (auth: E), H (auth: D)
Chain Length:231
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:THSC20.HVTR26 (Fab26) - Light Chain
Chain IDs:E (auth: I), G (auth: H), I (auth: G)
Chain Length:216
Number of Molecules:3
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Cryo-EM reveals conformational variability in the SARS-CoV-2 spike protein RBD induced by two broadly neutralizing monoclonal antibodies.
Rsc Adv 15 14385 14399 (2025)
PMID: 40330036 DOI: 10.1039/d5ra00373c

Abstact

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.

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Protein

Chemical

Disease

Primary Citation of related structures
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