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- EMDB-61340: Engineering of ATP synthase Fo -

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Basic information

Entry
Database: EMDB / ID: EMD-61340
TitleEngineering of ATP synthase Fo
Map data
Sample
  • Complex: Bacillus PS3 FoF1
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase gamma chain
    • Protein or peptide: ATP synthase epsilon chain
    • Protein or peptide: ATP synthase subunit b
    • Protein or peptide: ATP synthase subunit c
KeywordsMolecular Motor / ATP synthase / MEMBRANE PROTEIN
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / lipid binding / ATP binding / plasma membrane
Similarity search - Function
ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily ...ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
ATP synthase gamma chain / ATP synthase epsilon chain / ATP synthase subunit c
Similarity search - Component
Biological speciesBacillus sp. PS3 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.96 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_61340.png

Downloads & links

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Map

FileDownload / File: emd_61340.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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0578
Minimum - Maximum-0.18574254 - 0.40777388
Average (Standard dev.)0.0012017601 (±0.008673002)
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_61340_msk_1.map
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Additional map: #1

Fileemd_61340_additional_1.map
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Half map: #2

Fileemd_61340_half_map_1.map
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Half map: #1

Fileemd_61340_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
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase gamma chain
    • Protein or peptide: ATP synthase epsilon chain
    • Protein or peptide: ATP synthase subunit b
    • Protein or peptide: ATP synthase subunit c

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Supramolecule #1: Bacillus PS3 FoF1

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

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Macromolecule #1: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 1
Details: based on pTR19-ASDS, which was created by Suzuki et al. (doi: 10.1074/jbc.M111210200)
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 26.44932 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEHKAPLVEF LGLTFNLSDM LMITITCLIV FIIAVAATRS LQLRPTGMQN FMEWVFDFVR GIINSTMDWQ TGGRFLTLGV TLIMYVFVA NMLGLPFSVH VNGELWWKSP TADATVTLTL AVMVVALTHY YGVKMKGASD YLRDYTRPVA WLFPLKIIEE F ANTLTLGL ...String:
MEHKAPLVEF LGLTFNLSDM LMITITCLIV FIIAVAATRS LQLRPTGMQN FMEWVFDFVR GIINSTMDWQ TGGRFLTLGV TLIMYVFVA NMLGLPFSVH VNGELWWKSP TADATVTLTL AVMVVALTHY YGVKMKGASD YLRDYTRPVA WLFPLKIIEE F ANTLTLGL RLFGNIYAGE ILLGLLASLG THYGVLGAVG AAIPMMVWQA FSIFVGTIQA FIFTMLTMVY MAHKVSHDH

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Macromolecule #2: ATP synthase gamma chain

MacromoleculeName: ATP synthase gamma chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 31.859523 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASLRDIKTR INATKKTSQI TKAMEMVSTS KLNRAEQNAK SFVPYMEKIQ EVVANVALGA GGASHPMLVS RPVKKTGYLV ITSDRGLAG AYNSNVLRLV YQTIQKRHAS PDEYAIIVIG RVGLSFFRKR NMPVILDITR LPDQPSFADI KEIARKTVGL F ADGTFDEL ...String:
MASLRDIKTR INATKKTSQI TKAMEMVSTS KLNRAEQNAK SFVPYMEKIQ EVVANVALGA GGASHPMLVS RPVKKTGYLV ITSDRGLAG AYNSNVLRLV YQTIQKRHAS PDEYAIIVIG RVGLSFFRKR NMPVILDITR LPDQPSFADI KEIARKTVGL F ADGTFDEL YMYYNHYVSA IQQEVTERKL LPLTDLAENK QRTVYEFEPS QEEILDVLLP QYAESLIYGA LLDAKASEHA AR MTAMKNA TDNANELIRT LTLSYNRARQ AAITQEITEI VAGANALQ

UniProtKB: ATP synthase gamma chain

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Macromolecule #3: ATP synthase epsilon chain

MacromoleculeName: ATP synthase epsilon chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 9.221647 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKTIHVSVVT PDGPVYEDDV EMVSVKAKSG ELGILPGHIP LVAPLEISAA RLKKGGKTQY IAVSGGFLEV RPDKVTILAQ AAERAED

UniProtKB: ATP synthase epsilon chain

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Macromolecule #4: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 4
Details: based on pTR19-ASDS, which was created by Suzuki et al. (doi: 10.1074/jbc.M111210200.)
Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 19.437396 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGEAAHGISG GTIIYQLLMF IILLALLRKF AWQPLMNIMK QREEHIANEI DQAEKRRQEA EKLLEEQREL MKQSRQEAQA LIENARKLA EEQKEQIVAS ARAEAERVKE TAKKEIEREK EQAMAALREQ VASLSVLIAS KVIEKELTEQ DQRKLIEAYI K DVQEVGGA R

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Macromolecule #5: ATP synthase subunit c

MacromoleculeName: ATP synthase subunit c / type: protein_or_peptide / ID: 5 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 7.33778 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSLGVLAAAI AVGLGALGAG IGNGLIVSRT IEGIARQPEL RPVLQTTMFI GVALVEALPI IGVVFSFIYL GR

UniProtKB: ATP synthase subunit c

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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

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: PDB ENTRY
PDB model - PDB ID:

6n2z

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32633
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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