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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 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: 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 ...

    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

    Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany. valentin.gordeliy@ibs.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit c, chloroplastic
A, B, C, D, E, F, G, H
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC (Subject of Investigation/LOI)
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
 Ligand Interaction
LFA (Subject of Investigation/LOI)
Query on LFA

Download Ideal Coordinates CCD File 
AA [auth H] , BA [auth H] , CA [auth H] , EA [auth I] , FA [auth I] , GA [auth J] , HA [auth L] , IA [auth L] , 
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
 Ligand Interaction
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

View Full Validation Report



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