Extended Data Figure 9: Simulation of STORM data using EM particle reconstruction data.

a, Left, end-on view of reconstructed TORC1 helix fitted with nine TORC1 particles in dark green, dark red, and purple (compare with Fig. 3). Middle, crystal structure of GFP (light green) was added to the reconstructed helix at sites identified as Raptor/Kog1 N termini. Right, crystal structure of anti-GFP nanobody (red) was added to a subset of the GFP structures, according to the labelling efficiency estimated for our experimental conditions (~20%). The localization precision is indicated as a red cloud. b, Three-dimensional representation of the simulated starting model according to a. Red and blue spheres denote GFP positions. c, Simulated STORM images. Helices of different lengths were generated on the basis of the distribution of focus sizes observed in vivo (Fig. 2 and bar graph). Orientations of these helices were randomized in three-dimensional (xyz) space and then projected in two-dimensions (xy). Coloured spheres denote GFP positions, a random fraction of which were considered labelled according to our experimentally determined labelling efficiency (see single-molecule localization microscopy simulation in Methods for more details). d, Reconstructions of individual simulations from c, classified according to their eccentricity and presence of a cavity. Scale bar, 100 nm. e, Particle averages obtained from the images in d. f, Plot of the eccentricity distribution of the simulated and experimental STORM dataset.