8H9S

Human ATP synthase state 1 (combined)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha, mitochondrialD [auth A],
E [auth B],
F [auth C]
510Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P25705 (Homo sapiens)
Explore P25705 
Go to UniProtKB:  P25705
PHAROS:  P25705
GTEx:  ENSG00000152234 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25705
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit beta, mitochondrialG [auth E],
H [auth F],
I [auth D]
482Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P06576 (Homo sapiens)
Explore P06576 
Go to UniProtKB:  P06576
PHAROS:  P06576
GTEx:  ENSG00000110955 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06576
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit gamma, mitochondrialJ [auth G]273Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P36542 (Homo sapiens)
Explore P36542 
Go to UniProtKB:  P36542
PHAROS:  P36542
GTEx:  ENSG00000165629 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36542
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATPase inhibitor, mitochondrialK [auth J]81Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UII2 (Homo sapiens)
Explore Q9UII2 
Go to UniProtKB:  Q9UII2
PHAROS:  Q9UII2
GTEx:  ENSG00000130770 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UII2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit O, mitochondrialL [auth O]190Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P48047 (Homo sapiens)
Explore P48047 
Go to UniProtKB:  P48047
PHAROS:  P48047
GTEx:  ENSG00000241837 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48047
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase F(0) complex subunit C1, mitochondrial75Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P05496 (Homo sapiens)
Explore P05496 
Go to UniProtKB:  P05496
PHAROS:  P05496
GTEx:  ENSG00000159199 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05496
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit delta, mitochondrialU [auth H]146Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P30049 (Homo sapiens)
Explore P30049 
Go to UniProtKB:  P30049
PHAROS:  P30049
GTEx:  ENSG00000099624 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30049
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit epsilon, mitochondrialV [auth I]51Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P56381 (Homo sapiens)
Explore P56381 
Go to UniProtKB:  P56381
PHAROS:  P56381
GTEx:  ENSG00000124172 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56381
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aW [auth N]226Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P00846 (Homo sapiens)
Explore P00846 
Go to UniProtKB:  P00846
PHAROS:  P00846
GTEx:  ENSG00000198899 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00846
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit ATP5MJ, mitochondrialX [auth P]58Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P56378 (Homo sapiens)
Explore P56378 
Go to UniProtKB:  P56378
PHAROS:  P56378
GTEx:  ENSG00000156411 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56378
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase protein 8Y [auth Q]68Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P03928 (Homo sapiens)
Explore P03928 
Go to UniProtKB:  P03928
PHAROS:  P03928
GTEx:  ENSG00000228253 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03928
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit f, mitochondrialZ [auth R]93Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P56134 (Homo sapiens)
Explore P56134 
Go to UniProtKB:  P56134
PHAROS:  P56134
GTEx:  ENSG00000241468 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56134
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit g, mitochondrialAA [auth S]102Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O75964 (Homo sapiens)
Explore O75964 
Go to UniProtKB:  O75964
PHAROS:  O75964
GTEx:  ENSG00000167283 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75964
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit e, mitochondrialBA [auth T]69Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P56385 (Homo sapiens)
Explore P56385 
Go to UniProtKB:  P56385
PHAROS:  P56385
GTEx:  ENSG00000169020 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56385
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

Download Ideal Coordinates CCD File 
CA [auth K],
OA [auth R]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
3PH (Subject of Investigation/LOI)
Query on 3PH

Download Ideal Coordinates CCD File 
NA [auth Q]1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
DA [auth A],
FA [auth B],
HA [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
JA [auth F],
LA [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
EA [auth A],
GA [auth B],
IA [auth C],
KA [auth F],
MA [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.53 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