Fig. 6: Template matching detects NPC subunits, microtubule protofilaments and ribosome-loaded vaults.

a, b Perspective view of the 3D constrained cross-correlation map obtained from template matching using an NPC subunit (a) and microtubule section (b). The templates are shown on the left-hand side of each panel. For the microtubule, two templates were used: a protofilament and an αβ-tubulin dimer. The 8- and 13-fold symmetries for the NPC and the microtubule, respectively, emerge naturally from template matching (zoom-ins with numbered peaks). Note that two NPCs at the edge of the lamella have only 7 (left) and 5 (center) detectable subunits left after the milling process. The NPC subunit and protofilament templates were cut from the whole NPC and microtubule templates, respectively. The αβ-tubulin dimers in (b) were obtained by masking the protofilament template (orange box). c From the 3D localization maps generated for visualization⁴ and analysis, TM finds ribosomes inside vaults indicated by the squares (i, ii and iii clockwise from left), see also Supplementary Fig. 14. In (i), the vault (magenta; z-score=\(54\)) containing the ribosome (green; z-score=\(63\)) is near a NPC (gray) and the nuclear envelope (purple). In (ii) and (iii), the vaults (z-score=\(32\) and z-score=\(59\)) containing the ribosomes (z-score=\(46\) and z-score=\(77\)) are in the cytoplasm. The templates used for the ribosome and the vault are identical to those used in Fig. 1. Here the vault is shown with a lower threshold level to visualize the ribosome on the inside.