Fig. 4: The Kappa variant S protein exhibits a novel dimer-of-trimers phenotype. | Nature Communications

Fig. 4: The Kappa variant S protein exhibits a novel dimer-of-trimers phenotype.

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

Fig. 4

a Side view of the global cryo-EM density map of the Kappa variant dimer-of-trimers complex. One trimer (S Protein 1, bottom) is displayed in various shades of blue, and the other trimer in grayscale (S Protein 2, top). b Focus-refined cryo-EM density map and fitted atomic model at the dimerisation interface. c Detailed view of the molecular interface between two RBDs in the grayscale trimer (top) and a single RBD in the blue shaded trimer (bottom). For amino acids involved in inter-residue hydrogen bonding, the backbone and sidechain atoms are displayed. Hydrogen bonds are indicated by yellow dashed lines. d The top-down view of the region in panel c is shown. The binding footprints of RBD1 and RBD2 are indicated by complementary shading and displaying the sidechain atoms of footprint residues.

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