EMD-39662

Single-particle
3.6 Å
EMD-39662 Deposition: 03/04/2024
Map released: 04/12/2024
Last modified: 04/12/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-39662

Vo domain of V/A-ATPase from Thermus thermophilus state2

EMD-39662

Single-particle
3.6 Å
EMD-39662 Deposition: 03/04/2024
Map released: 04/12/2024
Last modified: 04/12/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Thermus thermophilus HB8
Sample: Vo domain of V/A-ATPase from thermus thermophilus.
Fitted models: 8yy0 (Avg. Q-score: 0.442)

Deposition Authors: Kishikawa J, Nishida Y, Nakano A, Yokoyama K
Rotary mechanism of the prokaryotic V o motor driven by proton motive force.
Kishikawa JI , Nishida Y, Nakano A, Kato T , Mitsuoka K , Okazaki KI , Yokoyama K
(2024) Nat Commun , 15 , 9883 - 9883
PUBMED: 39567487
DOI: doi:10.1038/s41467-024-53504-x
ISSN: 2041-1723
Abstract:
ATP synthases play a crucial role in energy production by utilizing the proton motive force (pmf) across the membrane to rotate their membrane-embedded rotor c-ring, and thus driving ATP synthesis in the hydrophilic catalytic hexamer. However, the mechanism of how pmf converts into c-ring rotation remains unclear. This study presents a 2.8 Å cryo-EM structure of the Vo domain of V/A-ATPase from Thermus thermophilus, revealing precise orientations of glutamate (Glu) residues in the c12-ring. Three Glu residues face a water channel, with one forming a salt bridge with the Arginine in the stator (a/Arg). Molecular dynamics (MD) simulations show that protonation of specific Glu residues triggers unidirectional Brownian motion of the c12-ring towards ATP synthesis. When the key Glu remains unprotonated, the salt bridge persists, blocking rotation. These findings suggest that asymmetry in the protonation of c/Glu residues biases c12-ring movement, facilitating rotation and ATP synthesis.