9U6K

Cryo-EM structure of the Vo domain of V/A-ATPase under pmf condition, State3B

Summary for 9U6K

• Entry DOI: 10.2210/pdb9u6k/pdb
• EMDB information: 63911
• Descriptor: V-type ATP synthase subunit I, V-type ATP synthase, subunit K (2 entities in total)
• Functional Keywords: atp synthase, v atpase, v1 atpase, motor protein
• Biological source: Thermus thermophilus HB8; More
• Total number of polymer chains: 13
• Total formula weight: 121926.36

Authors

Nakano, A.,Kishikawa, J.,Nishida, Y.,Shigematsu, H.,Gerle, C.,Mitsuoka, M.,Yokoyama, K. (deposition date: 2025-03-23, release date: 2025-10-29)

Primary citation

Nakano, A.,Kishikawa, J.I.,Yui, N.,Sugawara, K.,Kan, Y.,Gerle, C.,Shigematsu, H.,Mitsuoka, K.,Yokoyama, K.
Structures of rotary ATP synthase from Thermus thermophilus during proton powered ATP synthesis.
Sci Adv, 11:eadx8771-eadx8771, 2025

PubMed Abstract: ATP synthases are rotary molecular machines that use the proton motive force to rotate the central rotor complex relative to the surrounding stator apparatus, thereby coupling the ATP synthesis. We reconstituted the V/A-ATPase into liposomes and performed structural analysis using cryo-EM under conditions where the proton motive force was applied in the presence of ADP and Pi. ATP molecules were bound at two of the three catalytic sites of V/A-ATPase, confirming that the structure represents a state adopted during ATP synthesis. In this structure, the catalytic site closes upon binding of ADP and Pi through an induced fit mechanism. Multiple structures were obtained where the membrane-embedded rotor ring was in a different position relative to the stator. By comparing these structures, we found that torsion occurs in both the central rotor and the peripheral stator during 31° rotation of rotor ring. These structural snapshots of V/A-ATPase provide crucial insights into the mechanism of rotary catalysis of ATP synthesis.

PubMed: 41105777
DOI: 10.1126/sciadv.adx8771

Experimental method

ELECTRON MICROSCOPY (4.1 Å)