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- EMDB-61342: Engineering of ATP synthase single stalk2 -

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Basic information

Entry
Database: EMDB / ID: EMD-61342
TitleEngineering of ATP synthase single stalk2
Map data
Sample
  • Complex: Bacillus PS3 FoF1
KeywordsMolecular Motor / ATP synthase / MEMBRANE PROTEIN
Biological speciesBacillus sp. PS3 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.64 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: Hiroshi Ueno / Kiyoto Yasuda / Norie Hamaguchi-Suzuki / Riku Marui / Naruhiko Adachi / Toshiya Senda / Takeshi Murata / Hiroyuki Noji /
Abstract: FF-ATP synthase (FF) interconverts the energy of the proton motive force (pmf) and that of ATP through the mechanical rotation. The H/ATP ratio, one of the most crucial parameters in bioenergetics, ...FF-ATP synthase (FF) interconverts the energy of the proton motive force (pmf) and that of ATP through the mechanical rotation. The H/ATP ratio, one of the most crucial parameters in bioenergetics, varies among species due to differences in the number of H-binding c-subunits, resulting in H/ATP ratios ranging from 2.7 to 5. In this study, we seek to significantly enhance the H/ATP ratio by employing an alternative approach that differs from that of nature. We engineer FF to form multiple peripheral stalks, each bound to a proton-conducting a-subunit. The engineered FF exhibits an H/ATP ratio of 5.8, surpassing the highest ratios found in naturally occurring FFs, enabling ATP synthesis under low pmf conditions where wild-type enzymes cannot synthesize ATP. Structural analysis reveals that the engineered FF forms up to three peripheral stalks and a-subunits. This study not only provides valuable insights into the H-transport mechanism of FF but also opens up possibilities for engineering the foundation of cellular bioenergetics.
History
DepositionAug 28, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61342.png

Downloads & links

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Map

FileDownload / File: emd_61342.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0433
Minimum - Maximum-0.16513214 - 0.37382364
Average (Standard dev.)0.0010655177 (±0.012736943)
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_61342_msk_1.map
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Additional map: #1

Fileemd_61342_additional_1.map
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Half map: #2

Fileemd_61342_half_map_1.map
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Half map: #1

Fileemd_61342_half_map_2.map
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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 198915
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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