9JC2 | pdb_00009jc2

Engineering of ATP synthase Fo


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.96 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit a
A, B, C
237Bacillus sp. PS3Mutation(s): 0 
UniProt
Find proteins for P09218 (Bacillus sp. (strain PS3))
Explore P09218 
Go to UniProtKB:  P09218
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09218
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase gamma chain285Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncGatpG
UniProt
Find proteins for P09222 (Bacillus sp. (strain PS3))
Explore P09222 
Go to UniProtKB:  P09222
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09222
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase epsilon chain87Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncCatpC
UniProt
Find proteins for P07678 (Bacillus sp. (strain PS3))
Explore P07678 
Go to UniProtKB:  P07678
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07678
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit b
F, G, H, I, J
F, G, H, I, J, K
169Bacillus sp. PS3Mutation(s): 0 
UniProt
Find proteins for P09221 (Bacillus sp. (strain PS3))
Explore P09221 
Go to UniProtKB:  P09221
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09221
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit c
L, M, N, O, P
L, M, N, O, P, Q, R, S, T, U
72Bacillus sp. PS3Mutation(s): 0 
Gene Names: atpEuncE
UniProt
Find proteins for P00845 (Bacillus sp. (strain PS3))
Explore P00845 
Go to UniProtKB:  P00845
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00845
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



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