8TM1 image
Entry Detail
PDB ID:
8TM1
EMDB ID:
Title:
Antibody N3-1 bound to RBDs in the up and down conformations
Biological Source:
PDB Version:
Deposition Date:
2023-07-27
Release Date:
2024-01-17
Method Details:
Experimental Method:
Resolution:
2.79 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Spike glycoprotein
Mutations:Hexapro construct
Chain IDs:A, B
Chain Length:1288
Number of Molecules:2
Biological Source:Severe acute respiratory syndrome coronavirus 2
Polymer Type:polypeptide(L)
Description:N3-1 Fab heavy chain
Chain IDs:C (auth: H)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:N3-1 Fab light chain
Chain IDs:D (auth: L)
Chain Length:108
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation

Abstact

The ongoing evolution of SARS-CoV-2 into more easily transmissible and infectious variants has provided unprecedented insight into mutations enabling immune escape. Understanding how these mutations affect the dynamics of antibody-antigen interactions is crucial to the development of broadly protective antibodies and vaccines. Here we report the characterization of a potent neutralizing antibody (N3-1) identified from a COVID-19 patient during the first disease wave. Cryogenic electron microscopy revealed a quaternary binding mode that enables direct interactions with all three receptor-binding domains of the spike protein trimer, resulting in extraordinary avidity and potent neutralization of all major variants of concern until the emergence of Omicron. Structure-based rational design of N3-1 mutants improved binding to all Omicron variants but only partially restored neutralization of the conformationally distinct Omicron BA.1. This study provides new insights into immune evasion through changes in spike protein dynamics and highlights considerations for future conformationally biased multivalent vaccine designs.

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Protein

Chemical

Disease

Primary Citation of related structures