In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges

Turoňová, Beata; Sikora, Mateusz; Schürmann, Christoph; Hagen, Wim J. H.; Welsch, Sonja; Blanc, Florian E. C.; Bülow, Sören von; Gecht, Michael; Bagola, Katrin; Hörner, Cindy; Zandbergen, Ger van; Mosalaganti, Shyamal; Schwarz, Andre; Covino, Roberto; Mühlebach, Michael D.; Hummer, Gerhard; Locker, Jacomine Krijnse; Beck, Martin

The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is required for cell entry and is the major focus for vaccine development. We combine cryo electron tomography, subtomogram averaging and molecular dynamics simulations to structurally analyze S in situ. Compared to recombinant S, the viral S is more heavily glycosylated and occurs predominantly in a closed pre-fusion conformation. We show that the stalk domain of S contains three hinges that give the globular domain unexpected orientational freedom. We propose that the hinges allow S to scan the host cell surface, shielded from antibodies by an extensive glycan coat. The structure of native S contributes to our understanding of SARS-CoV-2 infection and the development of safe vaccines. The large scale tomography data set of SARS-CoV-2 used for this study is therefore sufficient to resolve structural features to below 5 [A]ngstrom, and is publicly available at EMPIAR-10453.