A 13-subunit c-ring in the Chlamydomonas chloroplast ATP synthase lowers the H⁺/ATP cost of carbon fixation

The chloroplast F ₁ F _o ATP synthase is a rotary motor that converts the light-driven proton-motive force into the chemical energy of ATP. The number of c-subunits in its rotor fixes the number of protons translocated per ATP formed, a fundamental parameter of bioenergetic systems. The reference spinach enzyme possesses fourteen c-subunits and a H ⁺ /ATP ratio of 4.67. Green algae additionally operate a carbon-concentrating mechanism that sustains CO ₂ fixation in water at a substantial cost in ATP, yet the structure of the algal motor, and whether its bioenergetic parameters differ from those of vascular plants, remains unresolved. Here, a 2.2 Å structure of the ATP synthase of Chlamydomonas reinhardtii reveals that the enzyme carries a thirteen-membered c-ring, the first departure from c ₁₄ in a chloroplast, and with a lower predicted H ⁺ /ATP ratio of 4.33. Ordered waters trace a Grotthuss proton relay through the membrane, where an insulating triad separates the proton loading and unloading sites and couples flux to rotation. A single substitution in the redox switching γ-subunit abolishes the contact with the catalytic β-subunit that idles the enzyme in darkness in vascular plants. These unique features of the algal ATP synthase lower the H ⁺ /ATP cost of carbon fixation in the light and facilitate acetate metabolism in the dark.