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A map of the structure of bacteriorhodopsin has been obtained using electron microscopy and diffraction [ 11. It shows a resolution of 3.5 A in a direction parallel to the membrane plane, but poorer than this perpendicular. The map shows many features well resolved from the main density of the seven a-helices, which we interpret as the bulky aromatic side-chains of phenylalanine, tyrosine and tryptophan as well as a very dense feature which is the Bionone ring of the retinal chromophore. Using these bulky side-chains as guide points and taking account of bulges in the helices that indicate smaller side-chains such as leucine, a complete atomic model for bacteriorhodopsin between amino acids 8 and 225 has been built. Twenty-one amino acids contributed by all seven helices surround the retinal, and 26 amino acids contributed by five helices form the proton channel. Ten of the amino acids in the middle of the Fig. 1. Artistic impression showing the relutionship between the key residiies Asp-tIS, Asp-%, Asp-212, Lys-216 and A%-82 and the retinul binding site, the proton chunnel unrl overall molecrrlur hoiindury for the ground stute of hucteriorhodopsiri . _ -proton channel are also part of the retinal-building site. The model also Drovides a useful basis for consideration of the The cytoplasm is at the top of the diab Tram.mechanism of proton pumping and the interpretation of the other experimental data. In particular, the structure suggests that the pK changes in the Schiff base must act as the means by which light energy is converted into proton-pumping pressure into the channel. Asp-96 is on the pathway from the cytoplasm t o the Schiff base and Asp-85 on the pathway from the Schiff base to the extracellular surface. A schematic diagram showing the relationship of the retinal building site to the key residues is shown in Fig. 1.

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