Snapshots of ATP-driven substrate translocation by the mitochondrial AAA+ protease AFG3L2

AFG3L2, located in the mitochondrial inner membrane, is an ATP-fueled protease responsible for protein degradation, and its dysfunction has been implicated in multiple neurodegenerative disorders. However, the structural basis underlying its ATP-driven substrate translocation remains incompletely understood. Here, we purified full-length human AFG3L2 and determined its cryo-EM structures in four distinct conformational states (Con1-Con4), revealing substrate engagement in the core catalytic domain despite weak EM density for its transmembrane domain. These structures display an asymmetric spiral-staircase architecture in which the six protomers are arranged around a central pore that accommodates a polypeptide substrate. The four conformational states jointly reveal a substrate translocation mechanism in which ATP binding by the uppermost protomer promotes substrate engagement, whereas ATP hydrolysis by the lowermost ATP-bound protomer leads to substrate release. Our findings provide snapshots of ATP-driven substrate translocation by AFG3L2 and refine the hand-over-hand translocation mechanism by revealing substrate capture and release during an ordered ATPase cycle.