2WIE

High-resolution structure of the rotor ring from a proton dependent ATP synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 
    0.235 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CVMClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

High-Resolution Structure of the Rotor Ring of a Proton-Dependent ATP Synthase.

Pogoryelov, D.Yildiz, O.Faraldo-Gomez, J.D.Meier, T.

(2009) Nat Struct Mol Biol 16: 1068

  • DOI: https://doi.org/10.1038/nsmb.1678
  • Primary Citation of Related Structures:  
    2WIE

  • PubMed Abstract: 

    The crystal structure of the c-ring from the proton-coupled F1Fo ATP synthase from Spirulina platensis is shown at 2.1-A resolution. The ring includes 15 membrane-embedded c subunits forming an hourglass-shaped assembly. The structure demonstrates that proton translocation across the membrane entails protonation of a conserved glutamate located near the membrane center in the c subunit outer helix. The proton is locked in this site by a precise hydrogen bond network reminiscent of that in Na+-dependent ATP synthases. However, the structure suggests that the different coordination chemistry of the bound proton and the smaller curvature of the outer helix drastically enhance the selectivity of the H+ site against other cations, including H3O+. We propose a model for proton translocation whereby the c subunits remain in this proton-locked state when facing the membrane lipid. Proton exchange would occur in a more hydrophilic and electrostatically distinct environment upon contact with the a subunit interface.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE C CHAIN
A, B, C, D, E
82Arthrospira platensisMutation(s): 0 
EC: 3.6.3.14
Membrane Entity: Yes 
UniProt
Find proteins for A5HEI4 (Arthrospira platensis HN01)
Explore A5HEI4 
Go to UniProtKB:  A5HEI4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5HEI4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CVM
Query on CVM

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth D]
EA [auth D]
CYMAL-4
C22 H40 O11
JRNQXDHDSXBSFV-WXFJLFHKSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A, B, C, D, E
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.36α = 90
b = 93.36β = 90
c = 257.4γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CVMClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-29
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary