6ZMR

Porcine ATP synthase Fo domain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.94 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 dimeric ATP synthase from bovine mitochondria.

Spikes, T.E.Montgomery, M.G.Walker, J.E.

(2020) Proc Natl Acad Sci U S A 117: 23519-23526

  • DOI: https://doi.org/10.1073/pnas.2013998117
  • Primary Citation of Related Structures:  
    6YY0, 6Z1R, 6Z1U, 6ZBB, 6ZG7, 6ZG8, 6ZIK, 6ZIQ, 6ZIT, 6ZIU, 6ZMR, 6ZNA, 6ZPO, 6ZQM, 6ZQN

  • PubMed Abstract: 

    The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial matrix via the proton inlet half channel proceeds via a Grotthus mechanism, and a similar mechanism may operate in the exit half channel. The structure has given information about the architecture and mechanical constitution and properties of the peripheral stalk, part of the membrane extrinsic region of the stator, and how the action of the peripheral stalk damps the side-to-side rocking motions that occur in the enzyme complex during the catalytic cycle. It also describes wedge structures in the membrane domains of each monomer, where the skeleton of each wedge is provided by three α-helices in the membrane domains of the b-subunit to which the supernumerary subunits e, f, and g and the membrane domain of subunit A6L are bound. Protein voids in the wedge are filled by three specifically bound cardiolipin molecules and two other phospholipids. The external surfaces of the wedges link the monomeric complexes together into the dimeric structures and provide a pivot to allow the monomer-monomer interfaces to change during catalysis and to accommodate other changes not related directly to catalysis in the monomer-monomer interface that occur in mitochondrial cristae. The structure of the bovine dimer also demonstrates that the structures of dimeric ATP synthases in a tetrameric porcine enzyme have been seriously misinterpreted in the membrane domains.


  • Organizational Affiliation

    The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, United Kingdom.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase protein 8A [auth 8]67Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q35914 (Sus scrofa)
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UniProt GroupQ35914
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase F(0) complex subunit C1, mitochondrial75Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A8D1N484 (Sus scrofa)
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UniProt GroupA0A8D1N484
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aJ [auth a]226Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q35915 (Sus scrofa)
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UniProt GroupQ35915
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase peripheral stalk-membrane subunit bK [auth b]214Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A8D0MI69 (Sus scrofa)
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UniProt GroupA0A8D0MI69
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit d, mitochondrialL [auth d]161Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A4X1V4B4 (Sus scrofa)
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UniProt GroupA0A4X1V4B4
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit e, mitochondrialM [auth e]70Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9MYT8 (Sus scrofa)
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UniProt GroupQ9MYT8
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit f, mitochondrialN [auth f]87Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q95339 (Sus scrofa)
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UniProt GroupQ95339
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase g subunitO [auth g]102Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F1SAK7 (Sus scrofa)
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UniProt GroupF1SAK7
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase j subunit (6.8PL)P [auth j]60Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A4X1TX70 (Sus scrofa)
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UniProt GroupA0A4X1TX70
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase membrane subunit DAPITQ [auth k]57Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A4X1TQQ5 (Sus scrofa)
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UniProt GroupA0A4X1TQQ5
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
R [auth f]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M3L
Query on M3L
B [auth K]
C [auth L]
D [auth M]
E [auth N]
F [auth O]
B [auth K],
C [auth L],
D [auth M],
E [auth N],
F [auth O],
G [auth P],
H [auth Q],
I [auth R]
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/M009858/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-09
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references
  • Version 1.2: 2020-09-30
    Changes: Database references