Fig. 2. Retinal conformation captured 1 ps after rhodopsin photoactivation using TR-SFX.

a, Changes in electron density. The retinal (RET) model (red) and the contoured grey mesh (at 2.7σ of the 2F_obs − F_calc electron density map) correspond to rhodopsin in the dark state obtained by SFX. The difference Fourier electron density (F_obs(light) − F_obs(dark) contoured at 3.8σ) around the C₁₁=C₁₂ bond of the polyene chain and the C₂₀ methyl show features appearing after 1 ps photoactivation in blue (positive density) that are correlated with disappearing features in gold (negative density), establishing that the chromophore has already isomerized. A negative density is also observed along C₈ and C₁₀ of the retinal polyene chain. b,c, The effect of retinal isomerization on the surrounding amino acid residues. The model of 1-ps-photoactivated rhodopsin (retinal in yellow; rhodopsin in orange and green) obtained from the extrapolated map 2F_ext − F_calc (21% photoactivation; Methods) superimposed to the dark-state model (retinal in red; rhodopsin in grey). The main chain C_ɑ atoms of the protein were used for the structural superposition. b, The difference electron density map (F_obs(light) − F_obs(dark), contoured at 3.4σ) shows the presence of positive and negative electron densities (blue and yellow) around specific amino acids such as Tyr268^6.51 of the binding pocket. The arrows illustrate shifts or rotations. c, The torsion of the retinal polyene chain at C₁₁–C₁₃ in the direction of Tyr268 (the π-system at the isomerizing bond of retinal (yellow model) is now rotated 90° with respect to that of the dark state⁴⁸ (red model) (Extended Data Fig. 6)) and the bending along C₆–C₁₁. Selected distances from retinal to rhodopsin residues are shown as grey dotted lines for the dark state and as blue dotted lines for the isomerized form.