The two chains are separated at the N-termini. Those helices are kinked or bent around Lys 23, and meet around Ile 40. At that point they start a left-handed coiled-coil. That straightens out to a short region of purely parallel chains (around 55-75), and then twists to a right-handed coiled coil towards the C-terminus. At the C-termini the chains have greatly different conformations, with one completely helical including a 90 degree bend towards F1. The other chain has residues 145-156 in an irregular conformation, bending back and not contacting F1.
Cryo-EM structures of the autoinhibited E. coli ATP synthase in three rotational states.
Sobti M, Smits C, Wong AS, Ishmukhametov R, Stock D, Sandin S, Stewart AG.
Elife. 2016 Dec 21;5. pii: e21598. doi: 10.7554/eLife.21598.