3UD0

ATP synthase C10 ring in proton-unlocked conformation at PH 5.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the c(10) ring of the yeast mitochondrial ATP synthase in the open conformation.

Symersky, J.Pagadala, V.Osowski, D.Krah, A.Meier, T.Faraldo-Gomez, J.D.Mueller, D.M.

(2012) Nat.Struct.Mol.Biol. 19: 485-491

  • DOI: 10.1038/nsmb.2284
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The proton pore of the F(1)F(o) ATP synthase consists of a ring of c subunits, which rotates, driven by downhill proton diffusion across the membrane. An essential carboxylate side chain in each subunit provides a proton-binding site. In all the stru ...

    The proton pore of the F(1)F(o) ATP synthase consists of a ring of c subunits, which rotates, driven by downhill proton diffusion across the membrane. An essential carboxylate side chain in each subunit provides a proton-binding site. In all the structures of c-rings reported to date, these sites are in a closed, ion-locked state. Structures are here presented of the c(10) ring from Saccharomyces cerevisiae determined at pH 8.3, 6.1 and 5.5, at resolutions of 2.0 Å, 2.5 Å and 2.0 Å, respectively. The overall structure of this mitochondrial c-ring is similar to known homologs, except that the essential carboxylate, Glu59, adopts an open extended conformation. Molecular dynamics simulations reveal that opening of the essential carboxylate is a consequence of the amphiphilic nature of the crystallization buffer. We propose that this new structure represents the functionally open form of the c subunit, which facilitates proton loading and release.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, Chicago, Illinois, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit C, mitochondrial
K, L, M, N, O
76Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: OLI1 (ATP9, OLI3, PHO2)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
ATP synthase (F1c10)
Find proteins for P61829 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P61829
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
K, L, M, N, O
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.200 
  • Space Group: P 42 2 2
Unit Cell:
Length (Å)Angle (°)
a = 54.159α = 90.00
b = 54.159β = 90.00
c = 245.392γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACphasing
HKL-2000data reduction
REFMACrefinement
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-04-18
    Type: Database references
  • Version 1.2: 2012-06-13
    Type: Database references