High resolution structure of bacteriorhodopsin determined by electron crystallography

Bacteriorhodopsin pumps protons from the cytoplasm to the outside of halobacteria, Halobacterium salinarium, by using absorbed light energy. The newly observed density map at 3 Angstrom resolution clarified nearly the entire structure; the resolution in the direction perpendicular to the membrane surface is 3.2 Angstrom. The new structure clearly indicates the proton transfer pathway in bacteriorhodopsin. In particular, the location of key aspartic acid and glutamic acid residues in the derived structural model suggested funneling structures with different designs for input and output of protons on the cytoplasmic and extracellular sides, respectively, of the protein. This paper describes the major differences between the model based on the new observation and the former model obtained through crystallographic refinement by Grigorieff et al. (J. Mol. Biol. 259; 393-421, 1996).