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Frame — 1BMF, bovine F₁-ATPase
F₁ catalytic head of ATP synthase from bovine heart — PDB 1BMF. The 3D backbone, AMP-PNP analog and Mg²⁺ are deposited coordinates. Residue numbers follow this data slice (1BMF author numbering with a 30000 offset). This is F₁, not F₀ — disclosed. 1BMF is an F₁-ATPase still (a hydrolysis-related snapshot); the movie on this page is the synthesis direction because binding-change is reversible — the deposit did not photograph ATP being made.Source: PDB 1BMF (Abrahams et al. 1994, Nature 370:621–628 · DOI 10.1038/370621a0)
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Overall reaction (physiological rotary cycle)
ADP + Pi + n H⁺(P) → ATP + H₂O + n H⁺(N). EC 7.1.2.2. A full 360° cycle visits three β sites. This page plays one 120° binding-change step and one condensation. F₀ proton flow is named here, not animated.Source: BRENDA EC 7.1.2.2 · binding-change: Abrahams et al. 1994
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Setup — AMP-PNP analog resident, catalytic β empty (real 1BMF)
Setup shows deposited AMP-PNP (non-hydrolyzable ATP analog) and Mg²⁺ as a dim reference overlay. The catalytic β used on screen is empty. The deposited ADP ligand is not the reactant — schematic ADP arrives in ①.Source: PDB 1BMF — AMP-PNP analog overlay; catalytic β empty by design
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① — ADP arrives at catalytic β
[schematic] ADP docks at the empty β, using the deposited ADP site as a seat. Arrival only — Pi is ②. AMP-PNP stays the analog, not the reactant.Source: registered schematic — empty β seat from PDB 1BMF; analog is not the reactant
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② — Pi arrives next to ADP β-O
[schematic] Inorganic phosphate docks beside ADP’s terminal oxygen. Arrival only. No Å on this schematic seat.Source: registered schematic — no Pi ligand in the empty-β seat; no Å claimed
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③ — γ subunit 120° (binding-change)
[schematic] Gold Cα = deposited γ (1BMF chain G), split from α/β. γ turns 120° about its long axis; α/β stay as a static mesh. In the enzyme, β open/loose/tight cycling moves with γ — that domain motion is not drawn, so do not remember “only γ turns.” 1BMF has no rotary trajectory — the turn is schematic. F₀ protons that drive γ in vivo are named, not drawn.Source: schematic rotation of deposited chain-G Cα — 1BMF is a still (Abrahams et al. 1994); no rotary trajectory deposited
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④ — ADP β-O attacks Pi → ATP + H₂O
[schematic] One arrow from ADP’s terminal oxygen toward Pi (not Pi flying onto ADP). In-place cross-fade to ATP and water. AMP-PNP is still the analog. This attack is phosphate bookkeeping, not the hard step of ATP synthesis — at the tight β site ΔG of condensation is near zero; Boyer binding-change (affinity cycling with γ) is the catalytic idea.Source: associative in-line SN2 — ADP O3B → Pi P; analog overlay remains PDB 1BMF AMP-PNP (PG⋯Mg 3.37 Å, PB⋯PG 2.91 Å deposited) · binding-change: Boyer via Abrahams/Walker 1994
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⑤ — ATP leaves catalytic β
[schematic] ATP leaves the β pocket. Water stays until ⑥.Source: display convention — product leave; water remains until the next step
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⑥ — H₂O leaves (other direction)
[schematic] Water leaves on a different vector from ATP. A full 360° cycle is named, not packed on this page.Source: display convention — separate exits; no external geometry claimed
Legend & Fidelity
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Mechanism fidelity — measured vs. inferred
Measured layer: protein Cα, AMP-PNP analog, Mg²⁺ (1BMF). Inferred layer: schematic ADP/Pi/ATP/H₂O at the empty β, γ 120° pose (same Cα, spun), condensation arrow. Å numbers on this page are deposited analog–metal distances (AMP-PNP PG⋯Mg 3.37 Å; PB⋯PG 2.91 Å), not schematic seats. The crystal is an F₁-ATPase still; the movie is synthesis because binding-change is reversible. The SN2 overlay is phosphate chemistry — Boyer affinity cycling is the catalytic idea. α/β stay; β open/loose/tight motion is not drawn.
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Why are ADP, Pi, ATP and H₂O “[schematic]”?
The reaction seat on this page is empty by design. AMP-PNP is a trapped analog, not the catalytic ATP product. Substrate poses are literature-based reconstructions and are labeled [schematic]. No Å is claimed for those seats.Source: PDB 1BMF AMP-PNP analog ≠ product
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α/β stay; γ turns 120° [schematic]
No β-barrel opening, no F₀ c-ring. γ Cα does turn 120° on this page — schematic, not a deposited trajectory. α/β stay as a static mesh; in the enzyme β open/loose/tight cycling moves with γ. Do not remember “only γ turns.”
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Controversy — rotary catalysis vs unisite
Binding-change (Boyer) plus the 1BMF asymmetric β occupancy (Walker) is textbook. Unisite catalysis exists in dilute F₁ without rotation; this page does not draw unisite. The 120° arrow is educational, not a measured angular trajectory.
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Physiological regulation
IF1 (ATPase inhibitor) and the proton-motive force gate hydrolysis vs synthesis. This page does not animate IF1. See Walker, Biochem Soc Trans 2013 (PMID:23863149).
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Kinetics scope
This tool animates one 120° step; it does not model timecourses, steady-state kinetics, or Km / kcat / Vmax. Compiled bovine F₁ turnover is order-10² s⁻¹ in the literature and is not re-measured here — see BRENDA EC 7.1.2.2. Pair with a kinetics chapter. Binding order on screen is educational staging.
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Sequence
Bovine F₁ α UniProt P19483 (1BMF entity 1, 510 aa) · F₁ β (catalytic) UniProt P00829 (entity 2, 482 aa) — SIFTS · NCBI taxonomy 9913 (Bos taurus). Residue numbers = this data slice (1BMF author + 30000 offset).
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Sources — bibliography of this page
S1 — PDB 1BMF: bovine F₁-ATPase; Abrahams et al. 1994, Nature 370:621–628, PMID:8065448, DOI 10.1038/370621a0 (RCSB primary citation)
S2 — Walker 2013, Biochem Soc Trans, PMID:23863149 (IF1 / pmf gating named, not drawn)
S3 — BRENDA EC 7.1.2.2 (compiled turnover order-10² s⁻¹; not re-measured here)
S4 — UniProt P19483 (F₁ α) · P00829 (F₁ β) — SIFTS on 1BMF
S5 — How this page is drawn: ADP/Pi/ATP/H₂O = [schematic] at empty β; AMP-PNP analog overlay (PG⋯Mg 3.37 Å, PB⋯PG 2.91 Å deposited); γ 120° = schematic rotation of deposited chain-G Cα, not a trajectory; 1BMF is an F₁-ATPase still, movie is synthesis; SN2 = phosphate bookkeeping, Boyer affinity cycling is the idea; screen = one 120° step, not 360°
› The 3D protein is real 1BMF F₁ with genuine AMP-PNP and Mg²⁺. ADP, Pi, ATP and H₂O are compact schematic molecules at the empty β and labeled [schematic]. Screen = one 120° step, not a 360° cycle.