Extended Data Fig. 6: Conformation of retinal after 1, 10 and 100 ps of rhodopsin photoactivation using TR-SFX, and Schiff base surroundings.

(a-f) Retinal conformational changes until 100 ps. a) The superimposition of the retinal TR-SFX models in the dark (red model) and 1 to 100 ps photoactivation time delays highlights the main differences: the cis-to-trans isomerization at C11-C12 and the concomitant rotation of the C20-methyl around C13. Beside a slight tilt of the β-ionone ring, another difference between 1 (yellow model), 10 (light blue) and 100 (green) ps-structures is a slight relaxation of the polyene chain towards planarity. b) Original electron density map around the retinal in the rhodopsin dark state obtained by SFX (2Fo-Fc map contoured at 2.5 rmsd) and the resulting refined model in red. c) Extrapolated electron density map around the retinal of 1 ps-photoactivated rhodopsin obtained by TR-SFX (2Fext-Fc map contoured at 1.9 rmsd) and the resulting refined model in yellow. d) Extrapolated electron density map around the retinal of 10ps-photoactivated rhodopsin obtained by TR-SFX (2Fext-Fc map contoured at 0.9 rmsd) and the resulting refined model in blue. e) Extrapolated electron density map around the retinal of 100 ps-photoactivated rhodopsin obtained by TR-SFX (2Fext-Fc map contoured at 1.9 rmsd) and the resulting refined model in green. f) Structure of rhodopsin after 1ps photoactivation (yellow model) obtained by TR-SFX (this study) compared to a cryo-trapped bathorhodopsin state (green model) and the dark state (red model). (g-h) Schiff base-counterion E113 and neighbouring water hydrogen bond network after 1 picosecond of photoactivation. Panel g: influence of the C11-C12 isomerization on the Schiff base conformation and distance to the counterion E113. The two models of rhodopsin are superimposed on the Cɑ atoms of the protein. Retinal after 1 ps of photoactivation (yellow (with orange K296^(7.43))) is showing an all-trans conformation and the C15 of the C14-C15-NZ plane at the SB displays a slight kick towards the extracellular space compared to the structure of the dark state (red). The counterion E113^(3.28) moves accordingly, in the same direction of about 0.2-0.3 Å. Panel h: of the two water molecules W03 and W04 which form a bridge between the counterion E113^(3.28) and M86^(2.53) (and also contacting A117^(3.32), F91^(2.58) and F116^(3.31), not shown), only W04 has gained order. The two rhodopsin molecules models (dark in red; 1 ps in yellow) are contoured with their respective electron density maps, in blue (2Fo-Fc contoured at 1.3 rmsd) and in orange (2Fextrapolated-Fc contoured at 1.3 rmsd). By Δt = 100 ps we observe a reset of the occupancy, which is similar to that of the dark state structure.