6B2Z | pdb_00006b2z

Cryo-EM structure of the dimeric FO region of yeast mitochondrial ATP synthase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.6 of the entry. See complete history

Literature

Atomic model for the dimeric FO region of mitochondrial ATP synthase.

Guo, H.Bueler, S.A.Rubinstein, J.L.

(2017) Science 358: 936-940

  • DOI: https://doi.org/10.1126/science.aao4815
  • Primary Citation Related Structures: 
    6B2Z, 6B8H

  • PubMed Abstract: 

    Mitochondrial adenosine triphosphate (ATP) synthase produces the majority of ATP in eukaryotic cells, and its dimerization is necessary to create the inner membrane folds, or cristae, characteristic of mitochondria. Proton translocation through the membrane-embedded F O region turns the rotor that drives ATP synthesis in the soluble F 1 region. Although crystal structures of the F 1 region have illustrated how this rotation leads to ATP synthesis, understanding how proton translocation produces the rotation has been impeded by the lack of an experimental atomic model for the F O region. Using cryo-electron microscopy, we determined the structure of the dimeric F O complex from Saccharomyces cerevisiae at a resolution of 3.6 angstroms. The structure clarifies how the protons travel through the complex, how the complex dimerizes, and how the dimers bend the membrane to produce cristae.


  • Organizational Affiliation
    • Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada.

Macromolecule Content 

  • Total Structure Weight: 384.62 kDa 
  • Atom Count: 21,436 
  • Modeled Residue Count: 2,996 
  • Deposited Residue Count: 3,632 
  • Unique protein chains: 10

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit c, mitochondrial76Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P61829 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP61829
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase protein 8DA [auth L],
K [auth A]
48Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00856 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP00856
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit aEA [auth M],
L [auth a]
249Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00854 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP00854
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit bFA [auth N],
M [auth b]
209Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05626 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP05626
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit d, mitochondrialGA [auth O],
N [auth d]
173Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P30902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit e, mitochondrialHA [auth P],
O [auth e]
49Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit f, mitochondrialIA [auth Q],
P [auth f]
95Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q06405 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit gJA [auth R],
Q [auth g]
106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit j, mitochondrialKA [auth S],
R [auth i]
59Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P81450 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit k, mitochondrialLA [auth T],
S [auth k]
68Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P81451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTcryoSPARC0.4.1
RECONSTRUCTIONcryoSPARC0.4.1
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP 81294
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103310
Simons FoundationUnited States349247

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-08
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Database references
  • Version 1.2: 2017-11-29
    Changes: Database references
  • Version 1.3: 2019-04-17
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-12-18
    Changes: Author supporting evidence, Other
  • Version 1.5: 2024-03-13
    Changes: Data collection, Database references
  • Version 1.6: 2025-05-28
    Changes: Data collection, Structure summary