Cryo-electron Microscopy Structure of S-Trimer, a Subunit Vaccine Candidate for COVID-19

Within a year after its emergence, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected over 100 million people worldwide, with a death toll over 2 million. Vaccination remains the best hope to ultimately put this pandemic to an end. In this study, using Trimer-Tag technology, we produced both wild-type (WT) and furin site mutant (MT) S-Trimers for COVID-19 vaccine studies. Cryo-electron microscopy (cryo-EM) structures of the WT and MT S-Trimers, determined at 3.2 Å and 2.6 Å, respectively, revealed that both antigens adopt a tightly closed conformation and their structures are essentially identical to that of the previously solved full-length WT S protein in detergent. The tightly closed conformation is stabilized by fatty acid and polysorbate 80 binding at the receptor binding domains (RBDs) and the N-terminal domains (NTDs), respectively. Additionally, we identified an important pH switch in the WT S-Trimer that shows dramatic conformational change and accounts for its increased stability at lower pH. These results validate Trimer-Tag as a platform technology in production of metastable WT S-Trimer as a candidate for COVID-19 subunit vaccine. IMPORTANCE An effective vaccine against SARS-CoV-2 is critical to end the COVID-19 pandemic. In this study, using Trimer-Tag technology, we were able to produce stable and large quantities of WT S-Trimer, a subunit vaccine candidate for COVID-19 with high safety and efficacy from animal and phase 1 clinical trial studies. Cryo-EM structures of the S-Trimer subunit vaccine candidate show that it predominately adopts a tightly closed prefusion state and resembles the native and full-length spike in detergent, confirming its structural integrity. WT S-Trimer is currently being evaluated in a global phase 2/3 clinical trial. Taking into account the published structures of the S protein, we also propose a model to dissect the conformation change of the spike protein before receptor binding.