Fig. 4: TM analysis of the seven-fold and nine-fold symmetric NPCs shows incomplete CR and NR ring architectures.
From: Nuclear pores safeguard the integrity of the nuclear envelope
a, Schematic showing the overall TM analysis workflow. Subvolumes containing NPCs of interest are extracted from tomograms and subjected to three TM runs, using the CR, IR and NR averages as the search templates. Ellipsoidal masks used for the TM runs are shown as grey transparent spheres around the averages. The positions of the peaks were extracted from the output cross-correlation (CC) score volumes (see Methods for details). For visualization of the peaks, ±15 z-stacks around the cross-correlation peaks are extracted, and maximum values along the z axis are presented as 3D plots. Based on the positions of the extracted peaks and corresponding template orientations, the maps of the templates are projected back to generate a pseudo-composite map (rightmost panel). b, Representative results of the TM analysis of a seven-fold symmetric NPC. 3D plots of the peaks and a pseudo-composite map are shown as in a. c, 3D histogram showing the number of seven-fold symmetric NPCs and their differing numbers of CR and NR peaks detected by the TM analysis (n = 24 NPCs). d, Representative results of the TM analysis of a nine-fold symmetric NPC. 3D plots of the peaks and pseudo-composite map as in a. e, Analysis as in c for the nine-fold symmetric NPCs with different numbers of CR and NR peaks (n = 20 NPCs). In the pseudo-composite maps in a and d, gaps in the ring architectures are indicated by red arrowheads. In c and e, bars that include the examples shown in a, b and d are indicated by green arrowheads.
