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TitleSARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode.
Journal, issue, pagesCommun Biol, Vol. 6, Issue 1, Page 1250, Year 2023
Publish dateDec 11, 2023
AuthorsJule Goike / Ching-Lin Hsieh / Andrew P Horton / Elizabeth C Gardner / Ling Zhou / Foteini Bartzoka / Nianshuang Wang / Kamyab Javanmardi / Andrew Herbert / Shawn Abbassi / Xuping Xie / Hongjie Xia / Pei-Yong Shi / Rebecca Renberg / Thomas H Segall-Shapiro / Cynthia I Terrace / Wesley Wu / Raghav Shroff / Michelle Byrom / Andrew D Ellington / Edward M Marcotte / James M Musser / Suresh V Kuchipudi / Vivek Kapur / George Georgiou / Scott C Weaver / John M Dye / Daniel R Boutz / Jason S McLellan / Jimmy D Gollihar /
PubMed AbstractThe 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 ...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.
External linksCommun Biol / PubMed:38082099 / PubMed Central
MethodsEM (single particle)
Resolution2.79 - 3.2 Å
Structure data

41374

8tm1

EMDB-41374, PDB-8tm1:
Antibody N3-1 bound to RBDs in the up and down conformations
Method: EM (single particle) / Resolution: 2.79 Å

41382

8tma

EMDB-41382, PDB-8tma:
Antibody N3-1 bound to RBD in the up conformation
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-41399: Antibody N3-1 bound to SARS-CoV-2 spike
Method: EM (single particle) / Resolution: 2.8 Å

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 spike / neutralizing antibody / RBD-directed antibody / quaternary epitope / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex

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