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

Experimental Data Snapshot

  • 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


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: https://doi.org/10.1016/j.jmb.2009.05.082
  • Primary Citation of Related Structures:  

  • 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, 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC89Ilyobacter tartaricusMutation(s): 0 
Gene Names: atpE
Membrane Entity: Yes 
Find proteins for Q8KRV3 (Ilyobacter tartaricus)
Explore Q8KRV3 
Go to UniProtKB:  Q8KRV3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8KRV3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on F09

Download Ideal Coordinates CCD File 
BB [auth E]
BC [auth R]
BD [auth i]
BE [auth v]
DB [auth F]
BB [auth E],
BC [auth R],
BD [auth i],
BE [auth v],
DB [auth F],
DC [auth S],
DD [auth j],
FB [auth G],
FC [auth T],
FD [auth k],
HB [auth H],
HC [auth U],
HD [auth l],
JB [auth I],
JC [auth V],
JD [auth m],
LB [auth J],
LC [auth a],
LD [auth n],
NB [auth K],
NC [auth b],
ND [auth o],
PB [auth L],
PC [auth c],
PD [auth p],
RB [auth M],
RC [auth d],
RD [auth q],
TA [auth A],
TB [auth N],
TC [auth e],
TD [auth r],
VA [auth B],
VB [auth O],
VC [auth f],
VD [auth s],
XA [auth C],
XB [auth P],
XC [auth g],
XD [auth t],
ZA [auth D],
ZB [auth Q],
ZC [auth h],
ZD [auth u]
C9 H20 O
Query on NA

Download Ideal Coordinates CCD File 
AB [auth E]
AC [auth R]
AD [auth i]
AE [auth v]
CB [auth F]
AB [auth E],
AC [auth R],
AD [auth i],
AE [auth v],
CB [auth F],
CC [auth S],
CD [auth j],
EB [auth G],
EC [auth T],
ED [auth k],
GB [auth H],
GC [auth U],
GD [auth l],
IB [auth I],
IC [auth V],
ID [auth m],
KB [auth J],
KC [auth a],
KD [auth n],
MB [auth K],
MC [auth b],
MD [auth o],
OB [auth L],
OC [auth c],
OD [auth p],
QB [auth M],
QC [auth d],
QD [auth q],
SA [auth A],
SB [auth N],
SC [auth e],
SD [auth r],
UA [auth B],
UB [auth O],
UC [auth f],
UD [auth s],
WA [auth C],
WB [auth P],
WC [auth g],
WD [auth t],
YA [auth D],
YB [auth Q],
YC [auth h],
YD [auth u]
Experimental Data & Validation

Experimental Data

  • 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
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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