2WGM

Complete ion-coordination structure in the rotor ring of Na-dependent F-ATP synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Complete Ion-Coordination Structure in the Rotor Ring of Na(+)-Dependent F-ATP Synthases.

Meier, T.Krah, A.Bond, P.J.Pogoryelov, D.Diederichs, K.Faraldo-Gomez, J.D.

(2009) J Mol Biol 391: 498

  • DOI: 10.1016/j.jmb.2009.05.082
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The membrane-embedded rotors of Na(+)-dependent F-ATP synthases comprise 11 c-subunits that form a ring, with 11 Na(+) binding sites in between adjacent subunits. Following an updated crystallographic analysis of the c-ring from Ilyobacter tartaricus ...

    The membrane-embedded rotors of Na(+)-dependent F-ATP synthases comprise 11 c-subunits that form a ring, with 11 Na(+) binding sites in between adjacent subunits. Following an updated crystallographic analysis of the c-ring from Ilyobacter tartaricus, we report the complete ion-coordination structure of the Na(+) sites. In addition to the four residues previously identified, there exists a fifth ligand, namely, a buried structural water molecule. This water is itself coordinated by Thr67, which, sequence analysis reveals, is the only residue involved in binding that distinguishes Na(+) synthases from H(+)-ATP synthases known to date. Molecular dynamics simulations and free-energy calculations of the c-ring in a lipid membrane lend clear support to the notion that this fifth ligand is a water molecule, and illustrate its influence on the selectivity of the binding sites. Given the evolutionary ascendancy of sodium over proton bioenergetics, this structure uncovers an ancient strategy for selective ion coupling in ATP synthases.


    Organizational Affiliation

    Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany. thomas.meier@biophys.mpg.de



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v
89Ilyobacter tartaricusMutation(s): 0 
Gene Names: atpE
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
Rotor (c11) of Na+-dependent F-ATP Synthase with complete ion-coördination structure
Find proteins for Q8KRV3 (Ilyobacter tartaricus)
Go to UniProtKB:  Q8KRV3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F09
Query on F09

Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v
NONAN-1-OL
C9 H20 O
ZWRUINPWMLAQRD-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.69α = 90
b = 139.28β = 118.4
c = 151.91γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2013-05-29
    Changes: Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance