9EVD | pdb_00009evd

In situ structure of the peripheral stalk of the mitochondrial ATPsynthase in whole Polytomella cells


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.60 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation   3D Report Full Report


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Literature

In situ structure and rotary states of mitochondrial ATP synthase in whole Polytomella cells.

Dietrich, L.Agip, A.A.Kunz, C.Schwarz, A.Kuhlbrandt, W.

(2024) Science 385: 1086-1090

  • DOI: https://doi.org/10.1126/science.adp4640
  • Primary Citation of Related Structures:  
    9EVD

  • PubMed Abstract: 

    Cells depend on a continuous supply of adenosine triphosphate (ATP), the universal energy currency. In mitochondria, ATP is produced by a series of redox reactions, whereby an electrochemical gradient is established across the inner mitochondrial membrane. The ATP synthase harnesses the energy of the gradient to generate ATP from adenosine diphosphate (ADP) and inorganic phosphate. We determined the structure of ATP synthase within mitochondria of the unicellular flagellate Polytomella by electron cryo-tomography and subtomogram averaging at up to 4.2-angstrom resolution, revealing six rotary positions of the central stalk, subclassified into 21 substates of the F 1 head. The Polytomella ATP synthase forms helical arrays with multiple adjacent rows defining the cristae ridges. The structure of ATP synthase under native operating conditions in the presence of a membrane potential represents a pivotal step toward the analysis of membrane protein complexes in situ.


  • Organizational Affiliation
    • Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt, Germany.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ASA-10: Polytomella F-ATP synthase associated subunit 10A [auth 0]82Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A5H1ZR95 (Polytomella sp. Pringsheim 198.80)
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UniProt GroupA0A5H1ZR95
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase associated protein ASA1B [auth 1]618Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for Q85JD5 (Polytomella sp. Pringsheim 198.80)
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UniProt GroupQ85JD5
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial F1F0 ATP synthase associated 32 kDa proteinC [auth 3]325Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for K0J903 (Polytomella sp. Pringsheim 198.80)
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UniProt GroupK0J903
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial F1F0 ATP synthase associated 14 kDa proteinD [auth 5]123Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for A0A024FSR7 (Polytomella sp. Pringsheim 198.80)
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UniProt GroupA0A024FSR7
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit ASA6E [auth 6]151Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for D7P897 (Polytomella sp. Pringsheim 198.80)
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UniProt GroupD7P897
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ATP synthase associated protein ASA7F [auth 7]190Polytomella sp. Pringsheim 198.80Mutation(s): 0 
UniProt
Find proteins for D8V7I2 (Polytomella sp. Pringsheim 198.80)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit ASA8G [auth 8]89Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D8V7I7 (Polytomella sp. Pringsheim 198.80)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ASA-9: Polytomella F-ATP synthase associated subunit 9H [auth 9]97Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A5H1ZR73 (Polytomella sp. Pringsheim 198.80)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ATP synthase subunit 6I [auth M]327Polytomella sp. Pringsheim 198.80Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for H8PGG3 (Polytomella sp. Pringsheim 198.80)
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UniProt GroupH8PGG3
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.60 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONCoot
MODEL REFINEMENTISOLDE

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
German Research Foundation (DFG)GermanyFOR2848

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release