6ZIT

bovine ATP synthase Stator domain, state 2


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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase protein 8A [auth 8]66Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P03929 (Bos taurus)
Explore P03929 
Go to UniProtKB:  P03929
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03929
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aB [auth a]226Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00847 (Bos taurus)
Explore P00847 
Go to UniProtKB:  P00847
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00847
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit d, mitochondrialC [auth d]160Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P13620 (Bos taurus)
Explore P13620 
Go to UniProtKB:  P13620
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13620
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit e, mitochondrialD [auth e]70Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q00361 (Bos taurus)
Explore Q00361 
Go to UniProtKB:  Q00361
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00361
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit f, mitochondrialE [auth f]87Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q28851 (Bos taurus)
Explore Q28851 
Go to UniProtKB:  Q28851
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ28851
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit g, mitochondrialF [auth g]102Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q28852 (Bos taurus)
Explore Q28852 
Go to UniProtKB:  Q28852
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ28852
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit ATP5MPL, mitochondrialG [auth j]60Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P14790 (Bos taurus)
Explore P14790 
Go to UniProtKB:  P14790
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14790
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase membrane subunit DAPIT, mitochondrialH [auth k]57Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q3ZBI7 (Bos taurus)
Explore Q3ZBI7 
Go to UniProtKB:  Q3ZBI7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3ZBI7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase F(0) complex subunit C2, mitochondrialI [auth R],
J [auth K],
K [auth L]
75Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07926 (Bos taurus)
Explore P07926 
Go to UniProtKB:  P07926
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07926
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase F(0) complex subunit B1, mitochondrialL [auth b]214Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P13619 (Bos taurus)
Explore P13619 
Go to UniProtKB:  P13619
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13619
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase-coupling factor 6, mitochondrialM [auth h]76Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P02721 (Bos taurus)
Explore P02721 
Go to UniProtKB:  P02721
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02721
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit O, mitochondrialN [auth S]190Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P13621 (Bos taurus)
Explore P13621 
Go to UniProtKB:  P13621
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13621
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha, mitochondrialO [auth C]510Bos taurusMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for P19483 (Bos taurus)
Explore P19483 
Go to UniProtKB:  P19483
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19483
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M3L
Query on M3L
I [auth R],
J [auth K],
K [auth L]
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

View Full Validation Report



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