-
Complex I — NADH dehydrogenase (shown in 3D, blue)
Respiratory Complex I (NADH:ubiquinone oxidoreductase) from Thermus thermophilus — 4HEA (Baradaran R, Berrisford JM, Minhas GS, Sazanov LA, Nature 2013, PMID:23934108). Real FMN cofactor, 8 iron–sulfur clusters (N1a/N1b/N3/N4/N5/N6a/N6b/N2) and the ubiquinone-binding cavity are shown. Overall: NADH + Q + 5H⁺N → NAD⁺ + QH₂ + 4H⁺P.
-
Complex III — cytochrome bc₁ (shown in 3D, orange)
Bovine mitochondrial cytochrome bc₁ complex — 1BGY (Iwata S et al., Science 1998, PMID:9560229). Real heme bL, bH, heme c₁ and the Rieske [2Fe–2S] cluster are shown. The Q-cycle (Qo oxidation, Qi reduction) is the essence: QH₂ + 2 cyt cox + 2H⁺N → Q + 2 cyt cred + 4H⁺P.
-
Complex IV — cytochrome c oxidase (shown in 3D, purple)
Bovine heart cytochrome c oxidase — 1OCC (Tsukihara T et al., Science 1996, PMID:8638158). Real CuA, heme a, and the heme a₃–CuB binuclear center where O₂ is reduced to water. Overall: 4 cyt cred + O₂ + 8H⁺N → 4 cyt cox + 2H₂O + 4H⁺P.
-
Complex V — ATP synthase (shown in 3D, green)
Bovine F₁-ATPase (α₃β₃γ) — 1BMF (Abrahams JP, Leslie AGW, Lutter R, Walker JE, Nature 1994, PMID:8065448). Real AMP-PNP and ADP in the catalytic β-sites. Proton-driven rotation of the γ rotor couples ADP + Pi → ATP (binding-change mechanism).
-
Complex II — succinate dehydrogenase (reference)
Complex II is the TCA enzyme succinate dehydrogenase (SDH) — already built as its own simulator (sdh.html, PDB 1ZOY). It feeds electrons (FADH₂) into the ubiquinone pool, bypassing Complex I.
-
Coupling & energy yield
Electron transfer releases energy to pump H⁺ across the inner membrane; the resulting proton-motive force drives Complex V. Per NADH ≈ 2.5 ATP, per FADH₂ ≈ 1.5 ATP (chemiosmotic theory; Mitchell 1961, PMID:13705192).
› The four 3D protein frames are real crystal structures (4HEA · 1BGY · 1OCC · 1BMF). Substrates/products (NADH, ubiquinone, cytochrome c, O₂, ATP) are drawn as compact schematic molecules and are labeled [schematic]; the H⁺ pumps and the proton gradient are shown as schematic arrows.