Extended Data Figure 3: Quantitative analysis of the mass and stoichiometry of the endogenous NPC (part 2).

a, Left, schematic localization of the Nup–GFP reporters selected for the in vivo calibrated imaging stoichiometry analyses. Nups were selected to represent every major NPC module and to provide comprehensive coverage of the assembly. Right, Kernel density estimation of distributions of GFP proteins per Nup were calculated from the calibrated imaging data. n?=?48–178. b, Heat map of a yeast cell expressing Nup85–GFP. Image (left) was acquired as described in Methods. In addition, for illustration purposes, a maximum projection along the z axis was performed, and the image was smoothed with a Gaussian blur of radius 1. A heat map was used to illustrate intensity units in raw photon counts. For the area outlined in a red rectangle, a 2D distribution of photon counts and the corresponding Gaussian fit are shown (right). c, Stoichiometries of main components associated with the affinity-captured NPCs, as determined by label-free mass spectrometry quantification (at least three peptides per protein). Proteins are grouped and coloured by functional categories or membership of discrete macromolecular assemblies. The TREX complex components are included in the ‘Transport & Associated Factors’ category and labelled with an asterisk. QconCAT-derived stoichiometries for all the Nups (dark grey bars) are shown for comparison.