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- PDB-9u6m: Cryo-EM structure of the Vo domain of V/A-ATPase under pmf condit... -

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Basic information

Entry
Database: PDB / ID: 9u6m
TitleCryo-EM structure of the Vo domain of V/A-ATPase under pmf condition, state3D
Components
  • V-type ATP synthase subunit I
  • V-type ATP synthase, subunit K
KeywordsMOTOR PROTEIN / ATP synthase / V ATPase / V1 ATPase
Function / homology
Function and homology information


proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / proton-transporting ATPase activity, rotational mechanism / ATPase binding
Similarity search - Function
V-type ATP synthase subunit I, N-terminal / Vacuolar ATPase subunit I, N-terminal proximal lobe / Vacuolar ATPase Subunit I N-terminal proximal lobe / V-type ATPase subunit I, N-terminal domain / V-ATPase proteolipid subunit / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
V-type ATP synthase subunit I / V-type ATP synthase, subunit K
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.64 Å
AuthorsNakano, A. / Kishikawa, J. / Nishida, Y. / Shigematsu, H. / Gerle, C. / Mitsuoka, M. / Yokoyama, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H02453 Japan
Japan Society for the Promotion of Science (JSPS)20K06514 Japan
Japan Agency for Medical Research and Development (AMED)JP17am0101001 Japan
CitationJournal: Sci Adv / Year: 2025
Title: Structures of rotary ATP synthase from during proton powered ATP synthesis.
Authors: Atsuki Nakano / Jun-Ichi Kishikawa / Nishida Yui / Kyosuke Sugawara / Yuto Kan / Christoph Gerle / Hideki Shigematsu / Kaoru Mitsuoka / Ken Yokoyama /
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 ...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.
History
DepositionMar 23, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N: V-type ATP synthase subunit I
O: V-type ATP synthase, subunit K
P: V-type ATP synthase, subunit K
Q: V-type ATP synthase, subunit K
R: V-type ATP synthase, subunit K
S: V-type ATP synthase, subunit K
T: V-type ATP synthase, subunit K
U: V-type ATP synthase, subunit K
V: V-type ATP synthase, subunit K
W: V-type ATP synthase, subunit K
X: V-type ATP synthase, subunit K
Y: V-type ATP synthase, subunit K
Z: V-type ATP synthase, subunit K


Theoretical massNumber of molelcules
Total (without water)122,39513
Polymers122,39513
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein V-type ATP synthase subunit I


Mass: 34679.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA1278 / Production host: Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SIT6
#2: Protein
V-type ATP synthase, subunit K


Mass: 7309.625 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA1277 / Production host: Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SIT7
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Vo domain of V/A-ATPase from Thermus thermophilus / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.66 MDa / Experimental value: YES
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Source (recombinant)Organism: Thermus thermophilus HB8 (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
4CTFFIND4.1.8CTF correction
7Coot0.9.4model fitting
8ISOLDE1.6model fitting
10PHENIX1.2model refinement
11cryoSPARC4.6initial Euler assignment
12cryoSPARC4.6final Euler assignment
13cryoSPARC4.6classification
14cryoSPARC4.63D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2094178
3D reconstructionResolution: 4.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29932 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6QUM

6qum


Accession code: 6QUM / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 304.67 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00328701
ELECTRON MICROSCOPYf_angle_d0.946711798
ELECTRON MICROSCOPYf_chiral_restr0.04621455
ELECTRON MICROSCOPYf_plane_restr0.00411487
ELECTRON MICROSCOPYf_dihedral_angle_d5.56591257

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