Structures and distributions of SARS-CoV-2 spike proteins on intact virions

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virions are surrounded by a lipid bilayer from which spike (S) protein trimers protrude¹. Heavily glycosylated S trimers bind the ACE2 receptor and mediate entry of virions into target cells^2–6. S exhibits extensive conformational flexibility: it modulates exposure of its receptor binding site and later undergoes complete structural rearrangement to drive fusion of viral and cellular membranes^2,7,8. The structures and conformations of soluble, overexpressed, purified S proteins have been studied in detail using cryo-electron microscopy^2,7,9–12. The structure and distribution of S on the virion surface, however, has not been characterized. Here we applied cryo-electron microscopy and tomography to image intact SARS-CoV-2 virions, determining the high-resolution structure, conformational flexibility and distribution of S trimers in situ on the virion surface. These results reveal the conformations of S present on the virion, and provide a basis from which to understand interactions between S and neutralizing antibodies during infection or vaccination.