Cryo-EM structure of the subunit a–c-ring complex. (A) The a–c complex is viewed from the mitochondrial matrix, i.e., the N side. The gray mesh is the cryo-EM map for subunit a; that for the c-ring is omitted for clarity. Red spheres indicate the Cα atoms of the conserved glutamate (Glu58) in the c-ring proton-binding sites. The dark and light blue spheres on subunit a indicate the conserved arginine (Arg145) in TM4 and the conserved glutamine (Gln201) in TM5. Green and yellow spheres indicate the positions in the E. coli subunit a for which a substituted cysteine is reactive with Cd²⁺, added from either the N or the P side, respectively, thereby blocking the proton transport mechanism (Gln201 is also a site of external Cd²⁺ block). (B) Same as A viewed along the membrane plane. (C–E) Smoothed surface of subunit a up to the Cγ atom of each side chain, colored as follows: blue, Lys or Arg; red, Asp, Glu, or His; green, polar; white, hydrophobic.