Cryo-EM structure of the SARS-CoV-2 omicron spike

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

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Omicron substitutions alter conformation and mobility of the RBD

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A subset of Omicron mutations changes the local conformation of spike

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The structure reveals the basis of antibody neutralization escape

SUMMARY

The recently reported B.1.1.529 omicron variant of 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 ? resolution cryo-electron 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.

Graphical AbstractKeywords

COVID-19

Omicron

B.1.1.529

neutralizing antibody

RBD

NTD

SARS-CoV-2

spike

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