Structural basis for prohibitin-mediated regulation of mitochondrial m-AAA protease

Mitochondrial function critically depends on protein quality control systems, with the m-AAA protease playing a key role at the inner mitochondrial membrane (IMM). The evolutionarily conserved prohibitins (PHBs) are essential modulators of this protease across species, yet the molecular mechanisms remain unclear. Here, we present the cryo-EM structure of the Chaetomium thermophilum PHB (CtPHB) complex, revealing a cage-like assembly composed of 11 copies of PHB1/PHB2 heterodimers. Electron microscopic and biochemical analyses suggest that m-AAA proteases are enclosed within the PHB complex through interactions mediated by their SPFH-interacting motif (SIM) exposed in the intermembrane space. Further in situ cryo-ET directly visualizes these cage-protease assemblies in native mitochondria. Disruption of their interface leads to elevated m-AAA protease activity and diminished mitochondrial stress resistance. These data establish PHB complexes as spatial organizers that compartmentalize m-AAA proteases in membrane microdomains to fine-tune proteolytic homeostasis. Our findings reveal the critical role of the PHB complex in maintaining mitochondrial proteostasis, providing a unified mechanistic model to explain and reconcile the pleiotropic and often contradictory phenotypes of PHB and m-AAA protease in mitochondrial physiology and various disease conditions. Mitochondrial protein quality control relies on the m-AAA protease, which is tightly regulated by prohibitins (PHBs). Here, authors reveal that PHBs assemble into a cage-like complex that encloses and spatially confines the m-AAA protease to fine-tune its activity and maintain mitochondrial proteostasis.