Fig. 2: Identification of COPII- and COPI-coated vesicles.

a, Gallery of x–y slices through COPII-coated vesicles from cryo-lamellae. The left panel shows an in vitro reconstituted vesicle for comparison¹⁶. Green rectangles are shown as rulers for coat thickness. Red arrowheads point to examples of outer coat. The right panels show partially coated vesicles, with the uncoated region highlighted in yellow. b, Gallery of x–y slices through COPI-coated vesicles from cryo-lamellae. The left panel shows an in vitro reconstituted vesicle for comparison²⁸. Magenta rectangles are shown as rulers for coat thickness. c, An x–y slice through an example of an uncoated vesicle. d, 3D rendering of segmented coated membranes are shown in pale green and purple depending on whether they were manually assigned to COPII or COPI, respectively. The highest cross-correlation peaks upon template matching using EMD-3968 as template (COPI structure) are shown as pink spheres, and those obtained with EMD-19417 as template (COPII structure) are shown in green. Template matching discriminates between the two classes of vesicles, and there is very good agreement with our previous manual assignment. Three example tomograms are shown. e, Top: slice through the y–z plane of the subtomogram average of particles picked from random oversampling of COPII-coated membranes, oriented normal to the membrane and aligned via shifts only. Middle: profile of an in vitro reconstituted sample, shown for comparison. Bottom: density profile obtained from the top panel. f, As in e, but for COPI. Panels are mirrored for clarity of comparison. Scale bars, 100 nm (a–d) (all panels) and 10 nm (e,f).