6YY0

bovine ATP synthase F1-peripheral stalk domain, state 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.23 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 subunit alpha, mitochondrial
A, B, C
510Bos taurusMutation(s): 2 
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit beta, mitochondrial
D, E, F
482Bos taurusMutation(s): 0 
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for P00829 (Bos taurus)
Explore P00829 
Go to UniProtKB:  P00829
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00829
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit gamma, mitochondrial273Bos 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit delta, mitochondrial146Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05630 (Bos taurus)
Explore P05630 
Go to UniProtKB:  P05630
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05630
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit epsilon, mitochondrial50Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05632 (Bos taurus)
Explore P05632 
Go to UniProtKB:  P05632
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05632
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATPase inhibitor, mitochondrial66Bos taurusMutation(s): 0 
Gene Names: ATPIF1ATPI
Membrane Entity: Yes 
UniProt
Find proteins for P01096 (Bos taurus)
Explore P01096 
Go to UniProtKB:  P01096
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01096
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit O, mitochondrialK [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: 8
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: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit d, mitochondrialM [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: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase-coupling factor 6, mitochondrialN [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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
O [auth A],
Q [auth B],
S [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
U [auth D],
W [auth E],
X [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
P [auth A],
R [auth B],
T [auth C],
V [auth D],
Y [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.23 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