6ZG7

bovine ATP synthase rotor domain, state 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.49 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 subunit gamma, mitochondrialA [auth G]273Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05631 (Bos taurus)
Explore P05631 
Go to UniProtKB:  P05631
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05631
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit delta, mitochondrialB [auth H]146Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05630 (Bos taurus)
Explore P05630 
Go to UniProtKB:  P05630
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UniProt GroupP05630
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit epsilon, mitochondrialC [auth I]50Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05632 (Bos taurus)
Explore P05632 
Go to UniProtKB:  P05632
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UniProt GroupP05632
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase F(0) complex subunit C2, mitochondrial75Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07926 (Bos taurus)
Explore P07926 
Go to UniProtKB:  P07926
Entity Groups  
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UniProt GroupP07926
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M3L
Query on M3L
D [auth R]
E [auth K]
F [auth L]
G [auth M]
H [auth N]
D [auth R],
E [auth K],
F [auth L],
G [auth M],
H [auth N],
I [auth P],
J [auth Q],
K [auth O]
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.17
MODEL REFINEMENTPHENIX1.18

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
Medical Research Council (MRC, United Kingdom)United KingdomMC_U105663150

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