Cell Reports
Volume 38, Issue 9, 1 March 2022, 110428
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Report
Cryo-EM structure of the SARS-CoV-2 Omicron spike

https://doi.org/10.1016/j.celrep.2022.110428Get rights and content
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Highlights

  • SARS-CoV-2 Omicron spike exclusively adopts a 1-RBD-up conformation

  • Omicron substitutions alter conformation and mobility of the RBD

  • A subset of Omicron mutations changes the local conformation of spike

  • The structure reveals the basis of antibody neutralization escape

Summary

The recently reported B.1.1.529 Omicron variant of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) includes 34 mutations in the spike protein relative to the Wuhan strain, including 15 mutations in the receptor-binding domain (RBD). Functional studies have shown Omicron to substantially escape the activity of many SARS-CoV-2-neutralizing antibodies. Here, we report a 3.1 Å-resolution cryoelectron microscopy (cryo-EM) structure of the Omicron spike protein ectodomain. The structure depicts a spike that is exclusively in the 1-RBD-up conformation with high mobility of RBD. Many mutations cause steric clashes and/or altered interactions at antibody-binding surfaces, whereas others mediate changes of the spike structure in local regions to interfere with antibody recognition. Overall, the structure of the Omicron spike reveals how mutations alter its conformation and explains its extraordinary ability to evade neutralizing antibodies.

Keywords

COVID-19
Omicron
B.1.1.529
neutralizing antibody
RBD
NTD
SARS-CoV-2
spike
variant of concern
cryo-EM

Data and code availability

  • Cryo-EM maps and fitted coordinates of Omicron spike have been deposited with accession code EMDB: EMD-25896 and PDB: 7THK, respectively.

  • This paper does not report original code.

  • Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

Cited by (0)

5

These authors contributed equally

6

Lead contact