The SARS-CoV-2 Spike harbours a lipid binding pocket which modulates stability of the prefusion trimer

Abstract

Large trimeric Spikes decorate SARS-CoV-2 and bind host cells via receptor binding domains (RBDs). We report a conformation in which the trimer is locked into a compact well-ordered form. This differs from previous structures where the RBD can flip up to recognise the receptor. In the locked form regions associated with fusion transitions are stabilised and the RBD harbours curved lipids. The acyl chains bind a hydrophobic pocket in one RBD whilst the polar headgroups attach to an adjacent RBD of the trimer. By functional analogy with enteroviral pocket factors loss of the lipid would destabilise the locked form facilitating receptor attachment, conversion to the postfusion state and virus infection. The nature of lipids available at the site of infection might affect the antigenicity/pathogenicity of released virus. These results reveal a potentially druggable pocket and suggest that the natural prefusion state occludes neutralising RBD epitopes, achieving conformational shielding from antibodies.

Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies

“…Binding by two samples was most affected by mutations in the core RBD epitope (Figure 3C). The sites where mutations reduced binding by these core-RBD targeting plasma clustered around the lipid-binding pocket in the RBD, where binding of free fatty acids may contribute to locking spike into a ''closed'' conformation (Carrique et al, 2020;Toelzer et al, 2020). Notably, for the sample from subject K (day 29), no single RBD mutation had more than a small effect on plasma antibody binding (Figures 2 and 3D).…”

SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses

“…Of the 15 Omicron changes in the RBD, nine map to the ACE2 binding footprint: K417N, G446S, S477N, E484A, Q493R, G496S, Q498R, N501Y, Y505H, with N440K and T478K just peripheral (Figures 2B and 2C). Additionally, mutations occur on the right flank: G339D, S371L, S373P, and S375F (Figure 2B), the last three of which are adjacent to a lipid-binding pocket (Figure S1B) (Toelzer et al, 2020;Carrique et al, 2020). This pocket has been seen occupied by a lipid similar to linoleic acid in an unusually rigid state of S, where all RBDs are found in a locked-down configuration stabilized by lipid-bridged quaternary interactions between adjacent RBDs.…”

The antigenic anatomy of SARS-CoV-2 receptor binding domain

“…Binding in the context of the trimeric spike On isolated stabilized spikes the RBD is found in two orientations; ''up'' and ''down'' (Yuan et al, 2017;Roy et al, 2020). Both of these form an ensemble of conformations, up conformations vary by up to 20 (Zhou et al, 2020) and down can include a tighter packed ''locked'' conformation (Ke et al, 2020;Toelzer et al, 2020;Carrique et al, 2020;Xiong et al, 2020). The structures we see by cryo-EM have the RBD in either the classic up or down conformation (see Figure 7A), although antibody binding sometimes introduces small perturbations in the RBD orientation.…”