Note that all animations show the same process seen from different camera positions. Solved structures of vATPase, AP2 complex and clathrin tripods were used to see how vATPase fits within the clathrin lattice, thus all proteins have their ‘true’ dimensions. The plasma membrane is depicted in light beige, clathrin triskelia in dark beige/brown; vATPase complex in gray (when inactive), light blue/gray/dark green (when active; dark green = V1H-subunit), AP2 complex in purple/blue/light green. The plasma membrane starts as a flat surface on which the clathrin triskelia begin forming the ring formation around the vATPase (in clockwise direction). Only two AP2 complexes are depicted: upon cargo (yellow) binding, the AP2 complex alters its structure and recruits clathrin triskelia that start the formation of a clathrin ring around the vATPase. For the clathin ring to be ‘closed’, the ‘last’ triskelion to be inserted into the ring collides (gets in direct contact) with the vATPase, namely its regulatory V1H-subunit. We hypothesize that the regulatory V1H-subunit needs to be displaced inwards, resulting in the inhibition of the stalk rotation and thus block of the vATPase activity. So, upon insertion of the last triskelion in the clathrin ring, the vATPase becomes inactive (shown by a loss of color). The mechanical work of the clathrin coat proteins results in the membrane being pulled in, and as vesicle formation progresses, more clathrin triskelia are added. After vesicle is endocytosed, the clathrin coat disassembles (i.e. clathrin and adaptor proteins dissociate from the newly-formed vesicle), and the vATPase becomes active again. For more details, see Construction of the animated 3D model in the Supplementary Methods. A detailed (zoomed) view of regulatory V1H-subunit displacement is shown in Video 4.