The density map reveals the paths of all seven of rhodopsin’s trans-membrane helices in the meta I state. There is clear continuous density for helix 8, and also density for the extracellular plug, the cytoplasmic loops, the first N-acetyl glucosamine group in the oligo-saccharides attached to Asn2 and Asn15, for all five tryptophan residues, and for the β-ionone ring. Since so many features are well-resolved in the density map of the photostationary state, we have fitted the co-ordinates of the X-ray structure of rhodopsin in its ground-state (10, PDB code 1GZM) to the map by hand, followed by real-space refinement in the program O, treating the entire ground-state structure as a rigid-body. The Cα trace of the ground-state structure fitted to the density map is shown in these figures.
We detect a strong density feature in a pocket between those molecules that lie along the in-plane 2-fold screw axes. This lies near the extracellular side of helices 6 and 7 of one molecule, and the intracellular side of helix 4 of the adjacent molecule. A possible candidate for this density is cholesterol. A cholesterol molecule (minus its hydrocarbon side-chain) can be fitted into the density feature. It is oriented with its tetracyclic fused ring system oriented normal to the plane of the crystal, which would be equivalent to an orientation normal to a membrane bilayer.