6CP3

Monomer yeast ATP synthase (F1Fo) reconstituted in nanodisc with inhibitor of oligomycin bound.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

High-resolution cryo-EM analysis of the yeast ATP synthase in a lipid membrane.

Srivastava, A.P.Luo, M.Zhou, W.Symersky, J.Bai, D.Chambers, M.G.Faraldo-Gomez, J.D.Liao, M.Mueller, D.M.

(2018) Science 360

  • DOI: https://doi.org/10.1126/science.aas9699
  • Primary Citation of Related Structures:  
    6CP3, 6CP5, 6CP6, 6CP7

  • PubMed Abstract: 

    Mitochondrial adenosine triphosphate (ATP) synthase comprises a membrane embedded F o motor that rotates to drive ATP synthesis in the F 1 subunit. We used single-particle cryo-electron microscopy (cryo-EM) to obtain structures of the full complex in a lipid bilayer in the absence or presence of the inhibitor oligomycin at 3.6- and 3.8-angstrom resolution, respectively. To limit conformational heterogeneity, we locked the rotor in a single conformation by fusing the F6 subunit of the stator with the δ subunit of the rotor. Assembly of the enzyme with the F6-δ fusion caused a twisting of the rotor and a 9° rotation of the F o c 10 -ring in the direction of ATP synthesis, relative to the structure of isolated F o Our cryo-EM structures show how F 1 and F o are coupled, give insight into the proton translocation pathway, and show how oligomycin blocks ATP synthesis.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Biology, Chicago Medical School, Rosalind Franklin University, 3333 Green Bay Road, North Chicago, IL 60064, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit 9, mitochondrial76Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit 5, mitochondrialK [auth Y]195Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P09457 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha, mitochondrialL [auth A],
M [auth B],
N [auth C]
510Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit beta, mitochondrialO [auth D],
P [auth E],
Q [auth F]
478Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit gamma, mitochondrialR [auth G]278Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit delta, mitochondrialS [auth H]138Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit epsilon, mitochondrialT [auth I]61Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit 4, mitochondrialU [auth Z]209Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit d, mitochondrialV [auth 7]173Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit H, mitochondrialW [auth 6]92Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit f, mitochondrialX [auth U]95Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase protein 8Y [auth 8]48Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aZ [auth X]249Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit J, mitochondrialAA [auth J]37Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
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Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A [auth K]
B [auth L]
C [auth M]
D [auth N]
E [auth O]
A [auth K],
B [auth L],
C [auth M],
D [auth N],
E [auth O],
F [auth P],
G [auth Q],
H [auth R],
I [auth S],
J [auth T]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.11.1
RECONSTRUCTIONRELION1.4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Health & Human Services (HHS)United StatesR01GM66223

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-23
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-15
    Changes: Author supporting evidence
  • Version 2.0: 2020-10-14
    Type: Coordinate replacement
    Reason: Atoms with unrealistic or zero occupancies
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Source and taxonomy, Structure summary