Extended Data Fig. 3: Subtomogram averaging of ribosomes.
From: In situ cryo-ET defines the ultrastructure of ER exit sites in human cells
a. An xy slice through a reconstructed tomogram, where ribosome density is visible. b. As in A, with ribosome cross-correlation peaks from PyTOM_TM in red. Inset: reference used for template matching. c. Starting reference for alignments in relion, obtained by averaging PyTOM_TM peaks and low-pass filtering at 150 Å. d. The map obtained after one round of 3D refinement in relion4. e. The map obtained after 5 rounds of refinement in WARP/M. f. The map in e, with a fitted atomic model (PDB 4ug0). g. The map in c was mirrored to obtain a new staring reference for 3D refinements in relion. h. The map obtained after one round of 3D refinement in relion against the mirrored starting reference, viewed in the same coordinate system (left) and rotated to match the view of the map in d. i. Top. Gold standard Fourier Shell Correlation between half maps from the 3D refinement in relion (map in panel d, dotted curve), and WARP/M (map in panel e, solid curve). Resolutions at 0.143 threshold are 20 and 15 Å respectively. Bottom. Map of ribosome coloured according to local resolution.
