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Frame — 1BGY, bovine cytochrome bc₁
Respiratory Complex III (ubiquinol–cytochrome c oxidoreductase) from bovine heart — PDB 1BGY. The 3D backbone, hemes bL / bH / c₁, and the Rieske [2Fe–2S] cluster are deposited coordinates. Residue numbers follow this data slice (1BGY author numbering with a 10000 offset). This is bovine, not bacterial or human CIII — disclosed under organism mixing.Source: PDB 1BGY (Iwata et al. 1998, Science · DOI:10.1126/science.281.5373.64)
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Overall reaction (full Q-cycle)
QH₂ + 2 cyt c(ox) + 2 H⁺(N) → Q + 2 cyt c(red) + 4 H⁺(P). EC 7.1.1.8. Crofts Q-cycle: Qo must oxidize QH₂ twice to make one QH₂ at Qi. This page plays one Qo oxidation (half-cycle). The second Qo pass is named here, not animated.Source: Crofts 2004 (Q-cycle) · BRENDA EC 7.1.1.8
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Setup — hemes + Rieske, Qo/Qi empty (real 1BGY)
Setup shows real heme bL, heme bH, heme c₁ and Rieske with both quinone pockets empty. No QH₂ at Qo, no Q at Qi.Source: PDB 1BGY — hemes + Rieske deposited; Qo/Qi quinones absent in this slice
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① — QH₂ arrives at Qo
[schematic] Hydroquinone cartoon of QH₂ (two phenols, two methoxy, short isoprene stub — not the C₁₀ tail) docks between heme bL and Rieske. 1BGY in this slice has no deposited Qo quinone. Docking only — the branch is ②.Source: registered schematic — no Qo quinone in this 1BGY slice; cleft from Iwata et al. 1998
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② — Qo branch — QH₂ → Rieske and QH₂ → bL
PROPOSAL [schematic] (hypothetical, lit.-based). One electron bead rides from a phenol oxygen to Rieske, one from the other phenol to heme bL. Both arrows start at QH₂ (not at bL). Two H⁺ leave the phenols toward the P-side — Qo chemistry in this half-cycle, not a separate pump step. Later steps split the two arms for reading; in the protein the Qo branch is nearly one event. QH₂ cross-fades to Q (carbonyls return). Qo semiquinone is debated in EPR (see controversy card); the textbook two-electron gate is still drawn, as a proposal. Two simultaneous hops, one event.Source: proposal — Q-cycle two-electron gate: Crofts 2004; Qo SQ EPR debated (controversy card)
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③ — Rieske → heme c₁
High-potential arm. The path marker rides Rieske FE1 → c₁ FE with the arrow. Nearest Fe–Fe from 1BGY: Rieske FE1–c₁ FE 27.01 Å — this crystal’s ISP pose, not the live tunneling distance after the swing. The Rieske ISP domain actually moves between Qo and c₁ in the crystal literature; this mesh is static, so that swing is not simulated.Source: Fe–Fe re-measured from PDB 1BGY · ISP swing named, not animated (Crofts 2004)
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④ — cyt c (ox) arrives at c₁
[schematic] Heme-c porphyrin cartoon of oxidized cytochrome c (Fe + porphyrin — not the protein fold) docks beside heme c₁. Arrival only — reduction is ⑤. In the mitochondrion cyt c is often already waiting; this late arrival is teaching order, not a kinetic claim. No cyt c ligand is in this 1BGY slice.Source: registered schematic — no cyt c in this 1BGY slice
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⑤ — heme c₁ reduces cyt c
[schematic] One electron bead rides heme c₁ Fe → heme-c Fe with the arrow; in-place ox→red cross-fade. A full Q-cycle reduces two cyt c; the second molecule needs a second Qo turnover (not on screen).Source: registered schematic — half-cycle honesty; full 2×Qo named in Overall reaction card · Crofts 2004
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⑥ — heme bL → heme bH
Low-potential arm. The electron bead rides deposited Fe to deposited Fe (bL FE–bH FE 20.30 Å). Separate event from the Qo branch. Qo cleft Rieske FE2–bL FE 31.05 Å (deposited; QH₂ seat itself has no Å).Source: Fe–Fe re-measured from PDB 1BGY
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⑦ — Q arrives at Qi
[schematic] Oxidized Q docks near heme bH. Arrival only. This Q is a different molecule from the Q still at Qo.Source: registered schematic — no Qi quinone in this 1BGY slice
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⑧ — bH reduces Q at Qi → SQ (one electron)
[schematic] One electron bead rides heme bH Fe onto a carbonyl oxygen of Q at Qi. The product is labeled SQ (one phenol, one carbonyl), not QH₂ — half-cycle honesty. A second Qo oxidation would deliver the second electron and make QH₂ at Qi (named, not on screen).Source: stoichiometric half-cycle label — not an EPR assignment · Q-cycle: Crofts 2004
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⑨ — Q leaves Qo; cyt c (red) leaves toward IV
[schematic] Two directions. SQ stays at Qi. The full cycle also takes 2 H⁺ from the N-side at Qi when the second electron makes QH₂ — those protons are not on this half-cycle screen. Net proton movement of a full Q-cycle is 4 H⁺ to the P-side, not the 2 H⁺ leaving Qo in ②. Complex IV chemistry lives on the CIV page; Complex II (SDH) is a separate simulator (sdh.html).Source: display convention — separate exits; no external geometry claimed · CIV etcc4.html · full-cycle protons: Crofts 2004
Legend & Fidelity
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Mechanism fidelity — measured vs. inferred
Measured layer: protein Cα, heme bL / bH / c₁, Rieske [2Fe–2S] (1BGY). Inferred layer: QH₂/Q/SQ benzoquinone cartoons, heme-c porphyrin cartoon, e⁻ beads riding each hop with the arrow (electrons are not particles on a wire — educational), two H⁺ leaving Qo phenols. Å numbers on this page are nearest-Fe distances between deposited cofactors (Rieske–bL 31.05 Å, Rieske–c₁ 27.01 Å, bL–bH 20.30 Å) in this ISP pose, not schematic seats and not the live swing distance. Screen protons at Qo are 2 H⁺; full-cycle net is 4 H⁺ to the P-side (Qi takes 2 H⁺ from the N-side on the second pass).
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Why are QH₂, Q, SQ and cyt c “[schematic]”?
This 1BGY data slice contains hemes and Rieske, not Qo/Qi quinones or cytochrome c. Substrate poses are literature-based reconstructions at the bL–Rieske cleft, the bH face, and the c₁ surface, and are labeled [schematic]. No Å is claimed for those seats.Source: PDB 1BGY ligands = hemes + Rieske only
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The protein mesh is static
No Rieske ISP domain swing (Qo ↔ c₁). That motion is crystallographically real and is named, not animated.
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Controversy — Qo semiquinone
The Q-cycle two-electron gate at Qo is textbook (Crofts). Stable detection of a Qo semiquinone by EPR is debated. This page draws the branch as PROPOSAL and does not assert a long-lived SQ at Qo. Qi SQ after one electron is a stoichiometric label for the half-cycle, not an EPR assignment.
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Physiological regulation
Complex III is inhibited by antimycin A (Qi) and myxothiazol / stigmatellin (Qo). This page does not animate inhibitors. See Crofts, Annu Rev Physiol 2004 (PMID:14977414).
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Kinetics scope
This tool animates one half Q-cycle; it does not model timecourses, steady-state kinetics, or Km / kcat / Vmax. Compiled bovine/human CIII turnover is order-10² s⁻¹ in the literature and is not re-measured here — see BRENDA EC 7.1.1.8. Pair with a kinetics chapter. Binding order on screen is educational staging.
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Sequence
Bovine cytochrome b UniProt P00157 (1BGY entity 3, hemes bL/bH) · cytochrome c₁ UniProt P00125 (entity 4) · Rieske ISP UniProt P13272 (entity 5) — SIFTS on 1BGY · NCBI taxonomy 9913 (Bos taurus)
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Sources — bibliography of this page
S1 — PDB 1BGY: bovine cytochrome bc₁; Iwata et al. 1998, Science 281:64–71, PMID:9651245, DOI 10.1126/science.281.5373.64 (RCSB primary citation)
S2 — Crofts 2004, Annu Rev Physiol, PMID:14977414 (Q-cycle; ISP swing named, not animated)
S3 — BRENDA EC 7.1.1.8 (compiled turnover order-10² s⁻¹; not re-measured here)
S4 — UniProt P00157 (cyt b) · P00125 (cyt c₁) · P13272 (Rieske) — SIFTS on 1BGY
S5 — How this page is drawn: QH₂/Q/SQ/cyt c = [schematic]; screen = one Qo oxidation, not 2 × Qo; ② Qo branch = PROPOSAL (nearly one event in the protein; later steps are split for reading); Fe–Fe Å from deposited 1BGY cofactors in this ISP pose; full-cycle Qi N-side 2 H⁺ named, not drawn
› The 3D protein is real 1BGY Complex III with genuine hemes and Rieske. QH₂, Q, SQ and cyt c are compact schematic molecules posed at the pockets and labeled [schematic]. Screen = one Qo oxidation, not 2 × Qo.