ENERGY, AT THE SMALLEST SCALE
Inside your mitochondria, a molecular machine turns a flow of protons into ATP, the energy currency of life.
This explorer uses the experimental bovine mitochondrial ATP synthase monomer structures 6ZPO, 6ZQM, and 6ZQN, determined by cryo-electron microscopy.
The primary view uses the actual 28 atom-derived protein surface meshes from the detailed film, reduced to about 220,000 triangles for the browser. The smoothed envelopes are not measured solvent-accessible surfaces. Cutaway reveals experimental backbone ribbons around the inner shaft, with deposited nucleotide atoms. States 2 and 3 use stator-aligned experimental backbone traces; they are not same-letter morphs of the film surfaces. Smooth motion and catalytic highlighting are mechanistic reconstructions, not molecular dynamics or observed turnover.
Author chain IDs are case sensitive. The rotor contains γ, δ, ε (G, H, I) and the c₈ ring (K–R). The α₃β₃ head (A–F) and peripheral stator (S, b, d, h: OSCP, b, d, F6) stay fixed. Subunit a and membrane accessories (8, e, f, g, j, k) are also fixed. In cutaway view, the front half of the surface envelope and membrane are removed while the head backbone remains visible around the shaft.
The deposited structures include inhibitor IF1 (chain J), which is omitted here to explain synthesis. Detailed waters and channel chemistry are omitted. The lipid bilayer follows the film’s curved, two-leaflet recipe, with paired bent tails and a viewing window around the membrane motor. The 40 Å head-center separation is a display recipe, not an experimentally located bilayer boundary. Protons enter and exit through separate half-channels in subunit a at the a/c-ring interface. They do not travel through the central shaft.
During synthesis, rotation drives the three β sites through binding, synthesis, and release. The gold site highlights and cycle labels illustrate that sequence. They do not describe the deposited occupancies: the inhibited structures have ADP in all three β chains and ATP in the noncatalytic α chains. The small nucleotide models show those actual deposited positions. An ideal full turn of the bovine c₈ ring couples eight protons to three ATP; this excludes additional mitochondrial transport costs. Proton-to-ATP ratios vary between organisms. ATP synthase can reverse to hydrolyze ATP and pump protons.
Spikes TE, Montgomery MG, Walker JE (2020). Structure of the dimeric ATP synthase from bovine mitochondria. PNAS 117, 23519–23526. Coordinate data: RCSB PDB / wwPDB, 6ZPO, 6ZQM, 6ZQN.
Renderer: Three.js (MIT). All app assets are served locally. No analytics, accounts, or uploads.
This interactive explorer needs JavaScript. ATP synthase uses the proton gradient across the inner mitochondrial membrane to rotate a c ring and central shaft, driving ATP synthesis in three β catalytic sites. Explore the experimental structure at RCSB PDB.