Prohibitin complexes associate with unique membrane microdomains in cells

Prohibitins are multi-subunit protein complexes implicated in a variety of roles in mitochondria, including maintaining cristae architecture, regulating lipid metabolism, and mediating protein quality control. Prohibitins form large, ring-like structures within the mitochondrial inner membrane, and it has been proposed that this unique architecture enables them to organize distinct membrane environments that support their diverse functions. However, the molecular mechanisms driving these structure-function relationships within the native cellular context remain poorly defined. In this work, we combine cellular cryo-electron tomography, subtomogram averaging, and Surface Morphometrics analysis to systematically characterize the structure and local membrane environment of prohibitin complexes in mouse embryonic fibroblast (MEF) cells. We show that prohibitins are enriched in the inner boundary membrane subdomain of the inner mitochondrial membrane. Moreover, we find that a subset of prohibitin complexes exhibits a unique association with a matrix-facing density that resembles an m-AAA protease. Further, we show that prohibitins consistently localize to regions of reduced lipid bilayer thickness across all inner mitochondrial membrane subdomains, suggesting that they locally remodel the membrane to support their function. Together, these findings provide direct structural evidence that prohibitin complexes are associated with unique membrane microdomains in cells and establish a framework for uncovering how the local cellular context enables prohibitin function.