Extended Data Fig. 9: Comparison of lateral fenestrations in microbial rhodopsins.

a–d, Surface representations of HeR (a), BR (b), XR (c, PDB code: 3DDL), and KR2 (d, PDB code: 3X3B). The side chains above the β-ionone ring are shown as sticks. e, f, Surface representations and cross sections of HeR (e) and metarhodopsin II intermediate (f, PDB code: 3PXO). Black arrows show two openings of the seven-transmembrane region. g–i, The difference UV–visible absorption spectra of wild-type HeR (i), HeR(G171W) (h) and GR (i) upon bleaching by 500 mM HA at different times in 20 mM HEPES–NaOH, pH 7.0, 100 mM NaCl and 0.1% DDM. j, Time evolution of the bleaching of the visible absorptions shown in g–i. The bleaching rate of the retinal chromophore in HeR is much faster than those in GR, suggesting that the retinal binding in HeR is not as tight as that in the type-1 rhodopsins. This observation is consistent with the fact that the residues constituting the retinal-binding site in HeR are smaller than those in the type-1 rhodopsins. These experiments were performed twice, and representative data are shown.