Significance
H
+
transport through the membrane-traversing F
1
F
0
ATP synthase mechanically drives bond formation between ATP and P
i
. For the enzyme in the inner membrane of
Escherichia coli
, we show here that the H
+
transport pathway extends beyond the lipid bilayer into cytoplasmic loops connecting transmembrane helices in both subunits
a
and
c
of the transmembrane F
0
sector. On the basis of chemical cross-linking, we postulate that the multiple loop regions functioning in H
+
transport pack into a single domain, which then interacts with the cytoplasmic surface of the H
+
channel within F
0
. The interaction of the loop regions with the H
+
channel is proposed to specifically gate H
+
release to the cytoplasmic side of the membrane during ATP synthesis.
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