9U6Q | pdb_00009u6q

Cryo-EM structure of the Vo domain of V/A-ATPase in liposomes under no pmf condition,state1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structures of rotary ATP synthase from Thermus thermophilus during proton powered ATP synthesis.

Nakano, A.Kishikawa, J.I.Yui, N.Sugawara, K.Kan, Y.Gerle, C.Shigematsu, H.Mitsuoka, K.Yokoyama, K.

(2025) Sci Adv 11: eadx8771-eadx8771

  • DOI: https://doi.org/10.1126/sciadv.adx8771
  • Primary Citation of Related Structures:  
    9U6F, 9U6G, 9U6H, 9U6I, 9U6J, 9U6K, 9U6L, 9U6M, 9U6N, 9U6O, 9U6P, 9U6Q, 9U6T, 9U6U, 9U6V, 9U6W, 9U6X, 9U6Y

  • 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.


  • Organizational Affiliation
    • Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto 603-8555, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase subunit IA [auth N]339Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA1278
UniProt
Find proteins for Q5SIT6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SIT6 
Go to UniProtKB:  Q5SIT6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SIT6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase, subunit K74Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA1277
UniProt
Find proteins for Q5SIT7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SIT7 
Go to UniProtKB:  Q5SIT7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SIT7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.2
RECONSTRUCTIONcryoSPARC4.6

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan23H02453
Japan Society for the Promotion of Science (JSPS)Japan20K06514
Japan Agency for Medical Research and Development (AMED)JapanJP17am0101001

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release