Extended Data Figure 3 : Electron density maps and crystal lattice.

From: Atomic structure of the eukaryotic intramembrane RAS methyltransferase ICMT

Extended Data Figure 3

a, Stereo representation of the electron density for the ICMT–monobody complex (blue mesh, 2FoFc, countoured at 1.1σ, calculated from 35 to 2.3 Å resolution) drawn around the atomic model (stick representation). The monobody is coloured magenta; ICMT is tan. b, Electron density for the lipid in the active site from a composite simulated-annealing omit-electron density map (2FoFc, contoured at 1σ and calculated from 35 to 2.3 Å resolution). The density would accommodate a geranylgeranyl lipid (orange sticks), as shown here. c, Electron density (blue mesh; 2FoFc map contoured at 1σ) for ordered monoolein lipids (magenta sticks) around ICMT. Monoolein lipids surround the transmembrane region of ICMT and collectively resemble a bilayer with typical thickness (arrows). The positioning of monoolein lipids in the vicinity of the M4–M5 connector (yellow) is consistent with the hypothesis that the enzyme would cause a slight depression in the membrane in this region, as illustrated in Extended Data Fig. 9. d, Crystal lattice in the ICMT–monobody complex, with ICMT coloured and the monobody in grey. e, A composite omit-electron-density map (2FoFc, contoured at 1σ and calculated from 35 to 4.0 Å resolution) for the X-ray structure of ICMT without the monobody. The composite omit maps, which reduce model bias, were obtained using Phenix36.