6TQJ

Crystal structure of the c14 ring of the F1FO ATP synthase from spinach chloroplast


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Unusual features of the c-ring of F1FOATP synthases.

Vlasov, A.V.Kovalev, K.V.Marx, S.H.Round, E.S.Gushchin, I.Y.Polovinkin, V.A.Tsoy, N.M.Okhrimenko, I.S.Borshchevskiy, V.I.Buldt, G.D.Ryzhykau, Y.L.Rogachev, A.V.Chupin, V.V.Kuklin, A.I.Dencher, N.A.Gordeliy, V.I.

(2019) Sci Rep 9: 18547-18547

  • DOI: https://doi.org/10.1038/s41598-019-55092-z
  • Primary Citation of Related Structures:  
    6TQJ

  • PubMed Abstract: 

    Membrane integral ATP synthases produce adenosine triphosphate, the universal "energy currency" of most organisms. However, important details of proton driven energy conversion are still unknown. We present the first high-resolution structure (2.3 Å) of the in meso crystallized c-ring of 14 subunits from spinach chloroplasts. The structure reveals molecular mechanisms of intersubunit contacts in the c 14 -ring, and it shows additional electron densities inside the c-ring which form circles parallel to the membrane plane. Similar densities were found in all known high-resolution structures of c-rings of F 1 F O ATP synthases from archaea and bacteria to eukaryotes. The densities might originate from isoprenoid quinones (such as coenzyme Q in mitochondria and plastoquinone in chloroplasts) that is consistent with differential UV-Vis spectroscopy of the c-ring samples, unusually large distance between polar/apolar interfaces inside the c-ring and universality among different species. Although additional experiments are required to verify this hypothesis, coenzyme Q and its analogues known as electron carriers of bioenergetic chains may be universal cofactors of ATP synthases, stabilizing c-ring and prevent ion leakage through it.


  • Organizational Affiliation

    Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit c, chloroplastic
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N
81Spinacia oleraceaMutation(s): 0 
Gene Names: atpH
Membrane Entity: Yes 
UniProt
Find proteins for P69447 (Spinacia oleracea)
Explore P69447 
Go to UniProtKB:  P69447
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69447
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download Ideal Coordinates CCD File 
DA [auth H](2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
LFA
Query on LFA

Download Ideal Coordinates CCD File 
AA [auth H]
BA [auth H]
CA [auth H]
EA [auth I]
FA [auth I]
AA [auth H],
BA [auth H],
CA [auth H],
EA [auth I],
FA [auth I],
GA [auth J],
HA [auth L],
IA [auth L],
JA [auth M],
KA [auth M],
LA [auth M],
MA [auth N],
NA [auth N],
O [auth A],
OA [auth N],
P [auth B],
Q [auth C],
R [auth C],
S [auth C],
T [auth D],
U [auth E],
V [auth F],
W [auth G],
X [auth G],
Y [auth G],
Z [auth H]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.136α = 90
b = 96.336β = 106.72
c = 158.684γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation16-15-00242
French National Research AgencyFranceANR-10-INSB-05-02
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)FranceANR-10-LABX-49-01
Russian Foundation for Basic ResearchRussian Federation18-34-00256

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description