Fig. 2: Structural comparisons of omicron open spike and prototypic open spike.

a Structural superimposition of the S1 subunits (without the RBDs) of omicron open spike and prototypic open spike from the top view. Prototypic spike is colored in gray. Omicron spike is colored by different subunits: subunit A contains the up-RBD and is colored in magenta, and subunits B and C contain the down-RBD and are colored in green and blue, respectively. The arrows indicate the domain shifting of the omicron spike relative to the prototypic spike. b Structural superimposition of the S1 subunit (without SD1 or SD2) of omicron open spike and prototypic open spike from the side view. The structures are colored in the same way as in panel (a). The interface between the NTD from subunit C and the RBD from subunit B is highlighted in the red circle. Because of domain shifting as shown in panel (a), the RBD/NTD interfaces are larger in the omicron open spike than in the prototypic open spike. c The S1/S2 structural interface in the omicron open spike from the side view. The structure is colored in the same way as in panel (a). Loop 853 (an S2 loop spanning residues 831–854) and Lys853 (which differs from the corresponding residue in the prototypic spike) are both colored in red. Loop 853 is partially disordered in the prototypic spike, but becomes ordered and mediates S1/S2 interactions in the omicron spike.