2X2V

Structural basis of a novel proton-coordination type in an F1Fo-ATP synthase rotor ring


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A New Type of Proton Coordination in an F(1)F(O)- ATP Synthase Rotor Ring.

Preiss, L.Yildiz, O.Hicks, D.B.Krulwich, T.A.Meier, T.

(2010) Plos Biol. 8: 443

  • DOI: 10.1371/journal.pbio.1000443

  • PubMed Abstract: 
  • We solved the crystal structure of a novel type of c-ring isolated from Bacillus pseudofirmus OF4 at 2.5 A, revealing a cylinder with a tridecameric stoichiometry, a central pore, and an overall shape that is distinct from those reported thus far. Wi ...

    We solved the crystal structure of a novel type of c-ring isolated from Bacillus pseudofirmus OF4 at 2.5 A, revealing a cylinder with a tridecameric stoichiometry, a central pore, and an overall shape that is distinct from those reported thus far. Within the groove of two neighboring c-subunits, the conserved glutamate of the outer helix shares the proton with a bound water molecule which itself is coordinated by three other amino acids of outer helices. Although none of the inner helices contributes to ion binding and the glutamate has no other hydrogen bonding partner than the water oxygen, the site remains in a stable, ion-locked conformation that represents the functional state present at the c-ring/membrane interface during rotation. This structure reveals a new, third type of ion coordination in ATP synthases. It appears in the ion binding site of an alkaliphile in which it represents a finely tuned adaptation of the proton affinity during the reaction cycle.


    Organizational Affiliation

    Department of Structural Biology, Max-Planck Institute of Biophysics, Frankfurt, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT C
A, B, C, D, E, F, G, H, I, J, K, L, M
69Bacillus pseudofirmus (strain OF4)Mutation(s): 0 
Gene Names: atpE
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
Rotor (c13) of H+-dependent F-ATP Synthase
Find proteins for P22483 (Bacillus pseudofirmus (strain OF4))
Go to UniProtKB:  P22483
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B, C, D, E, F, H, I, J, K, L
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
DPV
Query on DPV

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M
dodecyl 2-(trimethylammonio)ethyl phosphate
dodecylphosphocholine
C17 H38 N O4 P
QBHFVMDLPTZDOI-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
A, B, C, D, E, F, G, H, I, J, K, L, M
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 74.180α = 90.00
b = 97.340β = 104.73
c = 121.240γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-18
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance