(A) A slice through a cellular tomogram containing a representative Golgi stack and (B) corresponding 3D segmentation, showing the native morphology of the ER (yellow), four cis cisternae (green), cis vesicles (light green), four medial cisternae (magenta), medial vesicles (light pink), the trans cisterna (blue), trans vesicles (light blue) and the TGN (purple). Other membranes, the nuclear envelope, nuclear pore complexes and ribosomes are shown in grey. (C–E) Slices through (C, C’) clathrin, (D, D’) COPII and (E, E’) COPI coated transport vesicles found within the tomograms. Panels C, D and E are slices through the centers of the vesicles. Panels C’, D’ and E’ are top slices through the coats of the same vesicles, showing characteristic structures of (C’) clathrin triskelions, (D’) the triangular Sec13/31 COPII lattice, and (E’) the dense COPI coat. (F–H) Slices through three COPI buds in different stages of maturation. Yellow arrowheads: cytoplasmic boundary of the coat, blue arrowheads: vesicle or bud membrane. Scale bars: 200 nm in A-B, 50 nm in C-H.