Extended Data Fig. 2: Data collection, processing, and model building for the AP2^core-heparin complex.

(a) SDS-PAGE gel of the AP2^core purification (left) and a schematic of the components used to make cryo-EM grids (right) (b) 2D class averages of the ‘clean’ dataset that was used for ab initio model generation. Two classes were found for further processing. (c) Final cryo-EM map of the ‘closed’ AP2-heparin complex colored by local resolution. Standard FSC plots (d) and directional FSC plots (e) are shown. (f) Final cryo-EM map of the ‘bowl’ AP2-heparin complex colored by local resolution. Note the µ2-CTD has been ejected from the complex and is not resolved in this map. Standard FSC plots (g) and directional FSC plots (h) are shown. (i) Pseudo-difference density map for the AP2 bowl complex made in Chimera and colored red to show density that cannot be accounted for by AP2. A region of low-resolution density is seen on the surface of α, corresponding to a known PIP2 binding site. Additional density is found at the α/σ2 interface. (j) Same analysis as done in (I), but for the closed AP2-heparin complex. (k) The N-terminus of ß2 packs into the [D/E]xxL[L/I] binding pocket on σ2 (yellow) (l) The structures of the closed AP2 (2VGL.pdb) and [D/E]xxL[L/I]-bound unlatched AP2 (2JKR.pdb) are shown aligned to the model for AP2-heparin. The closed heparin structure shows an intermediate conformation between the closed apo and [D/E]xxL[L/I]-cargo bound states.