Fig. 1: Structural and molecular basis of the enhanced receptor binding in SARS-CoV-2 KP.3.

a Convergent emergence of SARS-CoV-2 RBD substitutions located on the receptor-binding interface (R346T, F456L, Q493E) in multiple JN.1-derived sublineages. b Percentage of JN.1 (F456 + Q493), JN.1 + F456L (Q493), JN.1 + Q493E (F456), and JN.1 + F456L + Q493E sequences from Jan 2024 to Aug 2024. Data were collected from GISAID. c SPR sensorgrams for the hACE2 binding of JN.1 and KP.3 Spike. Representative results of two replicates are shown. d Overall structures of JN.1-Q493E RBD, KP.2 RBD, KP.3 RBD in complex with hACE2. Purple, pink, green cartoons represent JN.1-Q493E, KP.2, KP.3 RBD respectively, blue color represents hACE2. Residues involved in interactions with hACE2 are shown as yellow balls. e Overall interactions of three variants RBDs with hACE2. Another view is available in Supplementary Fig. S3. Contacting residues are shown as sticks and H-bonds are shown as yellow dotted lines. Hydrophobic interactions are shown as semi-transparent gray regions. f Comparations of interfaces around site 456 and 493 of JN.1 RBD–hACE2 (8Y18), JN.1-Q493E RBD–hACE2, KP.2 RBD–hACE2, KP.3 RBD–hACE2 complexes. Gray cartoons represent JN.1 RBD, other colors indicate as in a. g Superimposition of hACE2-binding interfaces of JN.1 RBD–hACE2 and KP.3 RBD–hACE2 complexes. The potential clash that limits side chain conformation is shown in yellow circles. h, Mutation-induced ACE2-binding affinity variation between different mutants computed with alchemical free energy calculation. i The free energy variation of the L-to-F mutation in capped residues (ACE-X-NME). The computed value of –2.8 kcal/mol agrees well with the experimental value of −3 kcal/mol. j In L-to-F mutations, leg-specific free energy changes along with the net variations of ACE2-binding affinities computed with the cycle-closure condition. The change of RBD-ACE2 binding affinity is estimated indirectly as the difference of free energy variations along the RBD–ACE2 complex leg and the solvated RBD leg, i.e., \({\Delta \Delta} G=\Delta {G}_{\rm{mutation},\,{\rm{complex}}}-\Delta {G}_{\rm{mutation},\,{\rm{RBD}}}\). k The simulation relaxed apo RBD with marks on the central 456 residue and its spatial neighbors contributing to stabilization effects. l The RBD–ACE2 complex with marks highlighting the stabilizing tyrosine residues and the cavity-forming (RBD) E493–K31 (ACE2) coordination.