Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape

Omicron SARS-CoV-2 is rapidly spreading worldwide. To delineate the impact of emerging mutations on spike’s properties, we performed systematic structural analyses on apo Omicron spike and its complexes with human ACE2 or S309 neutralizing antibody (NAb) by cryo-EM. The Omicron spike preferentially adopts the one-RBD-up conformation both before and after ACE2 binding, which is in sharp contrast to the orchestrated conformational changes to create more up-RBDs upon ACE2 binding as observed in the prototype and other four variants of concern (VOCs). Furthermore, we found that S371L, S373P and S375F substitutions enhance the stability of the one-RBD-up conformation to prevent exposing more up-RBDs triggered by ACE2 binding. The increased stability of the one-RBD-up conformation restricts the accessibility of S304 NAb, which targets a cryptic epitope in the closed conformation, thus facilitating the immune evasion by Omicron. These results expand our understanding of Omicron spike’s conformation, receptor binding and antibody evasion mechanism.

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S304 and S309 mAbs targeting the SARS-CoV-2 spike protein were expressed in transient mammalian expression system and purified for structural determination in this study.
The S304 and S309 mAbs were expressed and purified in this study according to PMID: 32422645. Detail information was described in the Methods section of the manuscript. The specifications of these two mAbs have been validated previously (PMID: 32422645).
HEK293F cell line was bought from Thermo Fisher Scientific. HEK293T and Vero cells were bought from ATCC.
No cell authentication method was used.
All cell lines tested negative for mycoplasma.
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