Structure and inhibition of SARS-CoV-2 spike refolding in membranes
Michael W. Grunst, Zhuan Qin, Esteban Dodero‐Rojas, Shilei Ding, Jérémie Prévost, Yaozong Chen, Yanping Hu, Marzena Pazgier, Shenping Wu, Xuping Xie, Andrés Finzi, José N. Onuchic, Paul C. Whitford, Walther Mothes, Wenwei Li
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein binds the receptor angiotensin converting enzyme 2 (ACE2) and drives virus-host membrane fusion through refolding of its S2 domain. Whereas the S1 domain contains high sequence variability, the S2 domain is conserved and is a promising pan-betacoronavirus vaccine target. We applied cryo-electron tomography to capture intermediates of S2 refolding and understand inhibition by antibodies to the S2 stem-helix. Subtomogram averaging revealed ACE2 dimers cross-linking spikes before transitioning into S2 intermediates, which were captured at various stages of refolding. Pan-betacoronavirus neutralizing antibodies targeting the S2 stem-helix bound to and inhibited refolding of spike prehairpin intermediates. Combined with molecular dynamics simulations, these structures elucidate the process of SARS-CoV-2 entry and reveal how pan-betacoronavirus S2-targeting antibodies neutralize infectivity by arresting prehairpin intermediates.