F0F1 ATPase - aka ATP Synthase

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I. Introduction

The Protein Data Bank describes ATP Synthase as consisting of two interconnecting rotary motors. 

For more information see Biochemistry Online: Chapter 8C-10: Proton Gradient Collapse and ATP synthesis - Structure

II. General Structure

A. F1 ATPase Matrix Chemical Motor

The matrix domain core consist of a repeating (alph-beta)3 structure ,     .

highlight F0 alpha subunits - red cartoon
highlight F0 beta subunits - orange cartoon

B. Rotor/Axle connecting F0 and F1

highlight Rotor gamma subunit - purple cartoon
highlight Rotor delta subunit connecting gamma and membrane domain - magenta cartoon
highlight Rotor epsilon subunit which runs across parallel to the membrane - medium orchid cartoon

C. F0 membrane Electric Motor

Proton transfer occurs across this domain which consists of 12 identical c subunits each with an Asp 61 involved in rotating interactions with an Arg 210 on subunit A (missing from this model).

highlight membrane domain with c subunits - yellow cartoon
The isolated membrane F0 domain (pdb id: 1C17) from E. Coli in complex with the A subunit. The Asps 61s are shown in sticks in F0. The A chain (fuchsia, not shown in the links above) is shown with Arg 271 interacting with Asp 61s on the c chains. This pdb files shows the full c helices not found in the complete model shown in the links above and below)
rotate to see top down view of membrane plane to better see the interaction between the A chain Arg 271 and the adjacent C chain Asp 61s
path for H+ proton flow from Arg 271 of the A chain through adjacent transmembreane c helices in the F0 membrane domain. The A chain amino acids include Gln 252, Asn 214, Asn 148, Asp 119, His 245, Glu 219, Ser 144 and Asn 238.

D. Stator and peripheral subunits affecting activity

Oligomycin A binds between the a and c subunits in the F0 domain and inhibits proton transport.  Inhibition requires a distal OSCP (Oligomycin-Sensitivity Conferring Protein which is analogous to the bacterial delta subunit), a stalk protein subunit distal to Fo which couples Fo and F1.

highlight OSCP - lime cartoon
highlight peripheral stalk and stator - green cartoon

Note the additional protein changes involved in the complex.