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- EMDB-61345: Engineering of ATP synthase Double stalks1,3 -

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Basic information

Entry
Database: EMDB / ID: EMD-61345
TitleEngineering of ATP synthase Double stalks1,3
Map data
Sample
  • Complex: Bacillus PS3 FoF1
KeywordsMolecular Motor / ATP synthase / MEMBRANE PROTEIN
Biological speciesBacillus sp. PS3 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsHamaguchi-Suzuki N / Ueno H / Yasuda K / Marui R / Adachi N / Senda T / Noji H / Murata T
Funding support Japan, France, 6 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP21H00388 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05624 Japan
Japan Society for the Promotion of Science (JSPS)JP23K18092 Japan
Human Frontier Science Program (HFSP)RGP0054/2020 France
Japan Agency for Medical Research and Development (AMED)JP23ama121013 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101071 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Engineering of ATP synthase for enhancement of proton-to-ATP ratio
Authors: Ueno H / Yasuda K / Hamaguchi-Suzuki N / Marui R / Adachi N / Senda T / Murata T / Noji H
History
DepositionAug 28, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61345.png

Downloads & links

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Map

FileDownload / File: emd_61345.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 400 pix.
= 300. Å		0.75 Å/pix.
x 400 pix.
= 300. Å		0.75 Å/pix.
x 400 pix.
= 300. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0432
Minimum - Maximum-0.16090816 - 0.29234967
Average (Standard dev.)0.0010701272 (±0.011240786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 300.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61345_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_61345_additional_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61345_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61345_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacillus PS3 FoF1

EntireName: Bacillus PS3 FoF1
Components
  • Complex: Bacillus PS3 FoF1

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Supramolecule #1: Bacillus PS3 FoF1

SupramoleculeName: Bacillus PS3 FoF1 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bacillus sp. PS3 (bacteria)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 3 / Number real images: 56081 / 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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 34429
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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