The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2

Abstract

The majority of currently circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viruses have mutant spike glycoproteins that contain the D614G substitution. Several studies have suggested that spikes with this substitution are associated with higher virus infectivity. We use cryo-electron microscopy to compare G614 and D614 spikes and show that the G614 mutant spike adopts a range of more open conformations that may facilitate binding to the SARS-CoV-2 receptor, ACE2, and the subsequent structural rearrangements required for viral membrane fusion.

Keywords: Coronavirus; D614G; SARS-CoV-2; cryo-EM; spike.

Fig. 1.

Space-filling representation of the two predominant open forms of G614 spike and the predominant closed form of D614 spike. The one- and two-RBD-erect forms of G614 spike make up 87% of particles, while the closed form represents 83% of the D614 spike particles in our previous study (5). The three subunits of spike are colored in blue, goldenrod, and rosy brown for G614 and in lighter shades of the same colors for D614. The molecule is viewed with its long axis vertical.

Fig. 2.

Structural differences between the G614 and D614 spike. (A) Bar diagram, showing domain connectivity of spike and locations of residues 614 and 854 (Top), with domains colored on single monomer of open spike trimer and other monomers shown in gray (Bottom). (B) Space-filling representation of the closed conformations of G614 and D614 spikes viewed down the threefold axis. The monomers are colored similarly to Fig. 1 and the positions of the NTD, NTD-associated subdomain (NTD-s), and the RBD are labeled for one monomer, with the vertical line emanating from the center of the trimer helping to distinguish the different conformations of the NTDs in the two structures; the trimers are aligned on the large S2 helix (residues 986 to 1032) of one monomer. (C–E) Interaction between S1 NTD-s of the erecting monomer with a segment of S2 domain from a neighboring chain. The overall spike structure is shown as a molecular surface with the two interacting domains, NTD-s and S2, from two adjacent monomers shown in rosy brown and yellow (C), with (D) a zoom of the NTD-s in cartoon representation with the two residues forming a salt bridge in the closed conformation in ball-and-stick representation. D also shows an overlay of the similar structures of the open (colored in gold) and closed (colored orange) forms of G614 with the open form of D614 (colored light blue). (E) An overlay of the distinct structures of the open (dark blue) and closed form (light blue) of D614.