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- PDB-9jc1: Engineering of ATP synthase -

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Basic information

Entry
Database: PDB / ID: 9jc1
TitleEngineering of ATP synthase
Components(ATP synthase ...) x 6
KeywordsMEMBRANE PROTEIN / Molecular Motor / ATP synthase
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / ATP hydrolysis activity / 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, 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, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit ...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, 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, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP synthase subunit alpha / ATP synthase gamma chain / ATP synthase subunit beta / ATP synthase epsilon chain
Similarity search - Component
Biological speciesBacillus sp. PS3 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsHamaguchi-Suzuki, N. / Ueno, H. / Yasuda, K. / Marui, R. / Adachi, N. / Senda, T. / Noji, H. / Murata, T.
Funding support Japan, France, 6items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: ATP synthase subunit beta
E: ATP synthase subunit beta
F: ATP synthase subunit beta
G: ATP synthase gamma chain
H: ATP synthase epsilon chain
I: ATP synthase delta subunit,ATP synthase subunit alpha,ATP synthase subunit alpha
J: ATP synthase delta subunit,ATP synthase subunit alpha,ATP synthase subunit alpha
K: ATP synthase delta subunit,ATP synthase subunit alpha,ATP synthase subunit alpha
A: ATP synthase subunit b
B: ATP synthase subunit b
C: ATP synthase subunit b
L: ATP synthase subunit b
M: ATP synthase subunit b
N: ATP synthase subunit b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)505,74119
Polymers505,21714
Non-polymers5245
Water00
1


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

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Components

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ATP synthase ... , 6 types, 14 molecules DEFGHIJKACMBLN

#1: Protein ATP synthase subunit beta / ATP synthase F1 sector subunit beta / F-ATPase subunit beta


Mass: 53424.625 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Gene: uncD, atpD / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0M4U1P9, H+-transporting two-sector ATPase
#2: Protein ATP synthase gamma chain / ATP synthase F1 sector gamma subunit / F-ATPase gamma subunit


Mass: 31859.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Gene: uncG, atpG / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M4TPJ7
#3: Protein ATP synthase epsilon chain / ATP synthase F1 sector epsilon subunit / F-ATPase epsilon subunit


Mass: 9221.647 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Gene: uncC, atpC / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M5MQR7
#4: Protein ATP synthase delta subunit,ATP synthase subunit alpha,ATP synthase subunit alpha / ATP synthase F1 sector subunit alpha / F-ATPase subunit alpha


Mass: 63248.145 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: based on pTR19-ASDS, which was created by Suzuki et al. (doi: 10.1074/jbc.M111210200),based on pTR19-ASDS, which was created by Suzuki et al. (doi: 10.1074/jbc.M111210200)
Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Gene: uncA, atpA / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0M3VGF9, H+-transporting two-sector ATPase
#5: Protein ATP synthase subunit b


Mass: 18601.707 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: the same molecule as chain B,L and N; the full sequence is MGEAAHGISGGTIIYQLLMFIILLALLRKFAWQPLMNIMKQREEHIANEIDQAEKRRQEA EKLLEEQRELMKQSRQEAQALIENARKLAEEQKEQIVASARAEAERVKETAKKEIEREKE ...Details: the same molecule as chain B,L and N; the full sequence is MGEAAHGISGGTIIYQLLMFIILLALLRKFAWQPLMNIMKQREEHIANEIDQAEKRRQEA EKLLEEQRELMKQSRQEAQALIENARKLAEEQKEQIVASARAEAERVKETAKKEIEREKE QAMAALREQVASLSVLIASKVIEKELTEQDQRKLIEAYIKDVQEVGGAR
Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Production host: Escherichia coli (E. coli)
#6: Protein ATP synthase subunit b


Mass: 19437.396 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: based on pTR19-ASDS, which was created by Suzuki et al. (doi: 10.1074/jbc.M111210200)
Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 5 molecules

#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
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: Bacillus PS3 FoF1 / Type: COMPLEX / Entity ID: #1-#4, #6, #5 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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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 defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 56081

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88259 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 74.93 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00428566
ELECTRON MICROSCOPYf_angle_d0.555138858
ELECTRON MICROSCOPYf_chiral_restr0.04434659
ELECTRON MICROSCOPYf_plane_restr0.00455121
ELECTRON MICROSCOPYf_dihedral_angle_d4.38584186

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