Extended Data Fig. 9: Molecular diffusion of the prohibitin complex model.

(a) 1-2: AlphaFold-predicted structures of the human prohibitins. Prohibitin 1 (PHB1, Uniprot P35232) and prohibitin 2 (PHB2, Uniprot Q99623) showing key domains – transmembrane (yellow), PHB (blue), and coiled-coil (orange). 3-4: AlphaFold-predicted structures coloured according to the pLDDT (dark blue: pLDDT > 90, light blue: 90 > pLDDT > 70, yellow: 70 > pLDDT > 50, orange: pLDDT < 50). (b) 1-2: AlphaFold-predicted model of the PHB1 (green) and PHB2 (white) dimer. Structural model (1). Electrostatic potential map (2). (c) 1–3: Placement of individual prohibitin molecules in the final cryo-EM map. The densities only fit a single prohibitin molecule each. Side view (1). Top view (2). Detailed view on the large density at the lipid bilayer fitting a single PHB domain (3). (d, e) Two models for the prohibitin complex used in molecular dynamics (MD) simulations (PHB1 in magenta, PHB2 in green). Preservation of the complex after 100 ns simulations is observed, with increased stability at individual coiled-coil domains and flexibility at N-terminus and PHB domains. (f) RMSD curves of the MD simulations. RMSD of the model shown in D converged to ~1.4 nm (1). RMSD of the model shown in E converged to ~1.6 nm (2). (g) Isosurface representations. Comparison of the cryo-EM-derived map and an MD-derived map after 100 ns, excluding lipids for a protein-only comparison. The MD model maintains structural similarities with the initial model, indicating overall preservation during MD.