9JC1 | pdb_00009jc1

Engineering of ATP synthase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Engineering of ATP synthase for enhancement of proton-to-ATP ratio.

Ueno, H.Yasuda, K.Hamaguchi-Suzuki, N.Marui, R.Adachi, N.Senda, T.Murata, T.Noji, H.

(2025) Nat Commun 16: 5410-5410

  • DOI: https://doi.org/10.1038/s41467-025-61227-w
  • Primary Citation of Related Structures:  
    9JC1, 9JC2

  • PubMed Abstract: 

    F o F 1 -ATP synthase (F o F 1 ) 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 F o F 1 to form multiple peripheral stalks, each bound to a proton-conducting a-subunit. The engineered F o F 1 exhibits an H + /ATP ratio of 5.8, surpassing the highest ratios found in naturally occurring F o F 1 s, enabling ATP synthesis under low pmf conditions where wild-type enzymes cannot synthesize ATP. Structural analysis reveals that the engineered F o F 1 forms up to three peripheral stalks and a-subunits. This study not only provides valuable insights into the H + -transport mechanism of F o F 1 but also opens up possibilities for engineering the foundation of cellular bioenergetics.


  • Organizational Affiliation

    Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan. hueno@g.ecc.u-tokyo.ac.jp.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit betaA [auth D],
B [auth E],
C [auth F]
484Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncDatpD
EC: 7.1.2.2
UniProt
Find proteins for A0A0M4U1P9 (Bacillus sp. (strain PS3))
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Go to UniProtKB:  A0A0M4U1P9
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UniProt GroupA0A0M4U1P9
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase gamma chainD [auth G]285Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncGatpG
UniProt
Find proteins for A0A0M4TPJ7 (Bacillus sp. (strain PS3))
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Go to UniProtKB:  A0A0M4TPJ7
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UniProt GroupA0A0M4TPJ7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase epsilon chainE [auth H]87Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncCatpC
UniProt
Find proteins for A0A0M5MQR7 (Bacillus sp. (strain PS3))
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UniProt GroupA0A0M5MQR7
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase delta subunit,ATP synthase subunit alpha,ATP synthase subunit alphaF [auth I],
G [auth J],
H [auth K]
580Bacillus sp. PS3Mutation(s): 3 
EC: 7.1.2.2
UniProt
Find proteins for A0A0M3VGF9 (Bacillus sp. (strain PS3))
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UniProt GroupA0A0M3VGF9
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit bI [auth A],
K [auth C],
M
169Bacillus sp. PS3Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit bJ [auth B],
L,
N
169Bacillus sp. PS3Mutation(s): 0 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP21H00388
Japan Society for the Promotion of Science (JSPS)JapanJP19H05624
Japan Society for the Promotion of Science (JSPS)JapanJP23K18092
Human Frontier Science Program (HFSP)FranceRGP0054/2020
Japan Agency for Medical Research and Development (AMED)JapanJP23ama121013
Japan Agency for Medical Research and Development (AMED)JapanJP21am0101071

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection, Database references