8H9R

Human ATP synthase state 3b subregion 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the human ATP synthase.

Lai, Y.Zhang, Y.Zhou, S.Xu, J.Du, Z.Feng, Z.Yu, L.Zhao, Z.Wang, W.Tang, Y.Yang, X.Guddat, L.W.Liu, F.Gao, Y.Rao, Z.Gong, H.

(2023) Mol Cell 83: 2137

  • DOI: https://doi.org/10.1016/j.molcel.2023.04.029
  • Primary Citation of Related Structures:  
    8H9E, 8H9F, 8H9G, 8H9I, 8H9J, 8H9K, 8H9L, 8H9M, 8H9N, 8H9P, 8H9Q, 8H9R, 8H9S, 8H9T, 8H9U, 8H9V

  • PubMed Abstract: 

    Biological energy currency ATP is produced by F 1 F o -ATP synthase. However, the molecular mechanism for human ATP synthase action remains unknown. Here, we present snapshot images for three main rotational states and one substate of human ATP synthase using cryoelectron microscopy. These structures reveal that the release of ADP occurs when the β subunit of F 1 F o -ATP synthase is in the open conformation, showing how ADP binding is coordinated during synthesis. The accommodation of the symmetry mismatch between F 1 and F o motors is resolved by the torsional flexing of the entire complex, especially the γ subunit, and the rotational substep of the c subunit. Water molecules are identified in the inlet and outlet half-channels, suggesting that the proton transfer in these two half-channels proceed via a Grotthus mechanism. Clinically relevant mutations are mapped to the structure, showing that they are mainly located at the subunit-subunit interfaces, thus causing instability of the complex.


  • Organizational Affiliation

    State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; Institute for Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase F(0) complex subunit B1, mitochondrialA [auth K]214Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P24539 (Homo sapiens)
Explore P24539 
Go to UniProtKB:  P24539
PHAROS:  P24539
GTEx:  ENSG00000116459 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24539
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase-coupling factor 6, mitochondrialB [auth L]108Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P18859 (Homo sapiens)
Explore P18859 
Go to UniProtKB:  P18859
PHAROS:  P18859
GTEx:  ENSG00000154723 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18859
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit d, mitochondrialC [auth M]160Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O75947 (Homo sapiens)
Explore O75947 
Go to UniProtKB:  O75947
PHAROS:  O75947
GTEx:  ENSG00000167863 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75947
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81520108019
National Natural Science Foundation of China (NSFC)China813300237
National Natural Science Foundation of China (NSFC)China32100976
National Natural Science Foundation of China (NSFC)China82222042

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-06-07
    Changes: Database references
  • Version 1.2: 2023-07-05
    Changes: Database references
  • Version 1.3: 2024-07-03
    Changes: Data collection