Overall subunit organization and structure of the ATP synthase complex (see text for references). The F₁ is based on the structures of Stock et al. [74] and Gibbons et al. [27] (α yellow, β red, γ blue, ε brown, and c subunits (black lines) within the membrane (the surfaces of which are indicated by the green rectangles). The subunits whose structures are not completely known are shown graphically. The transport essential carboxylic acid of the c subunits are indicated by the “-“ symbols in red circles. The proposed H⁺ or Na⁺ channels are indicated by the yellow (outwards) and green (matrix or cytoplasmic) cylinders, with the conserved and essential a subunit Arg residue indicated by the “+” in blue.

Key residues contributing to the three catalytic sites. A. Overlay of the residues in β_TP (in CPK colors) and β_DP sites (in yellow). Bound ATP or ADP and Mg²⁺ are in black. B. The same amino acids in β_E. Note the difference in positions 32 of certain amino acids, in particular αArg376 (E. coli numbering) and αSer347 (red in β_TP, green in β_DP and β_E), which indicate the more open β_E conformation [2].

Model for partial reaction steps during rotational catalysis based on the kinetic model of Baylis Scanlon et al. [52]. The model explicitly denotes the binding of ATP to the site in the β_HC conformer [25], the reversible hydrolysis/synthesis occurring in the β_TP site, and the release of product Pi and ADP from β_E. Note that the 80° rotation of the γ subunit (eccentric in the middle of the trimer of the β subunit conformers) is associated with ATP binding or release, and the 40° rotation, k_γ, is the rate limiting step. The central blue arrows indicate the counter-clockwise rotation in hydrolysis. Notice that the “offset” indicates a 120° rotation in the counter-wise direction in hydrolysis, or 120° rotation in the clockwise direction in synthesis.

Ribbon diagram of the bovine heart mitochondrial F₁ based on [2]. A. From the “bottom”, or membrane facing side, of the F₁ complex. α subunits are in gray, β_TP in yellow, β_DP in red, β_E in blue, and γ in the surface model showing electrostatic potential (blue is negative, red is positive and white is apolar). B. From the “side” of the complex showing only the γ subunit in relationship to two of the β subunit conformers, β_DP (red) with bound ADP (in CPK colors), and β_E (blue). Note that the lower portion of the β_E subunit is swung outwards which results in an open conformation of the nucleotide binding catalytic site.

The rotation of the β subunit conformers during rotational catalysis. In looking at the F₁ from the “bottom” or membrane oriented side of the complex, rotation of the γ subunit is counter-clockwise for ATP hydrolysis, and clockwise in ATP synthesis (see [9] for a review). Note the order of the conformations in hydrolysis is β_E→β_TP→β_DP, and in synthesis is β_E→β_DP→β_TP.