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- EMDB-63913: Cryo-EM structure of the Vo domain of V/A-ATPase under pmf condit... -

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Basic information

Entry
Database: EMDB / ID: EMD-63913
TitleCryo-EM structure of the Vo domain of V/A-ATPase under pmf condition, state3D
Map data
Sample
  • Complex: Vo domain of V/A-ATPase from Thermus thermophilus
    • Protein or peptide: V-type ATP synthase subunit I
    • Protein or peptide: V-type ATP synthase, subunit K
KeywordsATP synthase / V ATPase / V1 ATPase / MOTOR PROTEIN
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)
Methodsingle 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, 3 items
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, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63913.png

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Map

FileDownload / File: emd_63913.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 336. Å		1.05 Å/pix.
x 320 pix.
= 336. Å		1.05 Å/pix.
x 320 pix.
= 336. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
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Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.2690825 - 0.76162916
Average (Standard dev.)-0.00030033148 (±0.038884696)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63913_msk_1.map
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Additional map: #1

Fileemd_63913_additional_1.map
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Additional map: including V1 region

Fileemd_63913_additional_2.map
Annotationincluding V1 region
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Half map: #1

Fileemd_63913_half_map_1.map
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Half map: #2

Fileemd_63913_half_map_2.map
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Sample components

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Entire : Vo domain of V/A-ATPase from Thermus thermophilus

EntireName: Vo domain of V/A-ATPase from Thermus thermophilus
Components
  • Complex: Vo domain of V/A-ATPase from Thermus thermophilus
    • Protein or peptide: V-type ATP synthase subunit I
    • Protein or peptide: V-type ATP synthase, subunit K

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Supramolecule #1: Vo domain of V/A-ATPase from Thermus thermophilus

SupramoleculeName: Vo domain of V/A-ATPase from Thermus thermophilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 660 KDa

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Macromolecule #1: V-type ATP synthase subunit I

MacromoleculeName: V-type ATP synthase subunit I / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 34.679383 KDa
Recombinant expressionOrganism: Thermus thermophilus HB8 (bacteria)
SequenceString: AKPFELLVSF LNTPKYGTFD PTPVVPVFFP FWFGMIVGDI GYALLFYLVG RWLSGYVKRN EPLVIDLFAL KLKPQVIGKL VHILNWMVF WTVVWGVIYG EFFGTFLEHL GVFGTPEHPG LIPILIHRID TAKTANLLIL LSVAFGVVLV FFGLALRAYL G LKHRHMAH ...String:
AKPFELLVSF LNTPKYGTFD PTPVVPVFFP FWFGMIVGDI GYALLFYLVG RWLSGYVKRN EPLVIDLFAL KLKPQVIGKL VHILNWMVF WTVVWGVIYG EFFGTFLEHL GVFGTPEHPG LIPILIHRID TAKTANLLIL LSVAFGVVLV FFGLALRAYL G LKHRHMAH FWEGVGYLGG LVGVLALAAS YLGNLQAGWL QGLMYLGFGV FLLAVLMSRI WLMIPEIFTQ AGHILSHIRI YA VGAAGGI LAGLLTDVGF ALAERLGLLG VLLGLLVAGV LHLLILLLTT LGHMLQPIRL LWVEFFTKFG FYEENG

UniProtKB: V-type ATP synthase subunit I

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Macromolecule #2: V-type ATP synthase, subunit K

MacromoleculeName: V-type ATP synthase, subunit K / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 7.309625 KDa
Recombinant expressionOrganism: Thermus thermophilus HB8 (bacteria)
SequenceString:
SGGLDRGLIA VGMGLAVGLA ALGTGVAQAR IGAAGVGAIA EDRSNFGTAL IFLLLPETLV IFGLLIAFIL NGRL

UniProtKB: V-type ATP synthase, subunit K

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 60000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2094178
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.8) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7vai

Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Number images used: 29932
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4.6)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6qum


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9u6m:
Cryo-EM structure of the Vo domain of V/A-ATPase under pmf condition, state3D

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