Fig. 5: Impact of residue identity at position 484 on S protein oligomerization. | Nature Communications

Fig. 5: Impact of residue identity at position 484 on S protein oligomerization.

From: Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants

Fig. 5

a Detailed view of the Kappa (B.1.617.1) dimer-of-trimers cryo-EM density map and fitted model at the Q484-Q484 interaction site. The hydrogen bond formed between Q484 residues located in different S ectodomain trimers (S protein 2 RBD 2 in black, and S protein 1 RBD 1 in cyan) is indicated with a yellow dashed line. b Cryo-EM density maps for the Kappa + Q484A and Kappa + Q484I mutated S proteins. c Summary table of the proportion of dimerised particles in S proteins harbouring mutations at position 484. Asterisks indicate structures reported in previous publications23. d E484, K484, and Q484 RBD electrostatic surface potentials highlighting the surface potentials at position 484. The E484 surface potential was generated using the previously reported wild-type (D614G) + ACE2 focus-refined atomic model23. The K484 surface potential was generated using the previously reported D614G + N501Y + E484K focus-refined atomic model23. The Q484 surface potential was generated using the Kappa + ACE2 focus-refined atomic model reported in the present manuscript.

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