Extended Data Fig. 2: Electron microscopy and 3D reconstructions for the tropisetron dataset (T), and for the serotonin + TMPPAA dataset (I2).

a, Tropisetron dataset (T). Selection of 2D class averages from the set of particles used for refinement of the tropisetron reconstruction. b, Three-dimensional reconstruction from the tropisetron dataset, filtered and coloured according to RELION local resolution. A global and a cut-through side view are shown. c, FSC curves for the density map before and after RELION post-processing, and between the model and the final map. d, Serotonin + TMPPAA dataset (I2). Selection of good 2D classes after one round of classification yields a set of 126,000 particles. One round of 3D classification with no symmetry imposed yields one class with pentameric symmetry, amounting to 62,000 particles. e, Unmasked unsharpened refined 3D reconstruction, filtered and coloured according to RELION local resolution. The colour range for resolution is similar to the equivalent representations for the other datasets in Extended Data Fig. 4c, allowing direct comparison. f, FSC curves for the density map before and after RELION post-processing, and between the model and the final map. g, Left, a non-sharpened map filtered at 3.9 Å resolution, obtained with a subset of 55,000 particles from the I2 dataset, selected after further 3D classification focused on the ICD. The hypothetical trajectory of the polypeptide chain after MX is bordered by a green line. No full connectivity can be visualized and the model was not built. The chain appears to descend abruptly after MX, and may interact with MA of the neighbouring subunit at the level of H411, where there is a clear density. Then it must link to the beginning of MA, but maps show no information how it may do so. The schematic representation highlights that this putative trajectory contacts MA on the neighbouring subunit close to residue H411. Right, the corresponding sharpened and masked reconstruction, showing that model building is not possible. The density of the disordered stretch closed to H411 is highlighted by the pink ellipses.