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Structure of the c10 ring of the yeast mitochondrial ATP synthase in the open conformation

Abstract

The proton pore of the F1Fo 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 c10 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.

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Figure 1: Structure of the c10 ring from yeast ATP synthase.
Figure 2: Structure of the c10 ring proton-binding site.
Figure 3: Protonation state of the binding site.
Figure 4: Simulations of the c10 ring in the lipid membrane and in the crystallization buffer.
Figure 5: Hypothetical rotary mechanism of proton translocation.

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Acknowledgements

The work was supported by a grant from the US National Institutes of Health R01GM66223 to D.M.M. T.M. and J.D.F.-G. are funded in part by the German Research Foundation Cluster of Excellence 'Macromolecular Complexes' (EXC115). Diffraction data were collected at the General Medicine and Cancer Institutes Collaborative Access Team (GM/CA-CAT) 23-ID and Southeast Regional Collaborative Access Team (SER-CAT) 22-ID beamlines at the Advanced Photon Source, Argonne National Laboratory. Use of the Advanced Photon Source was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, under contract number W-31-109-Eng-38. Computational resources were provided in part by the Jülich Supercomputing Center. We thank the reviewer for recognizing that residues 15–18 form a 310 helix.

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J.S. collected and analyzed diffraction data and collaborated in writing the manuscript. V.P. and D.O. designed and conducted experiments and aided in collecting diffraction data. J.D.F.-G. designed the research, analyzed data and collaborated in writing the manuscript. A.K. conducted the research and analyzed data. T.M. analyzed data and collaborated in writing the manuscript. D.M.M. designed experiments, analyzed data, aided in collecting diffraction data and collaborated in writing the manuscript.

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Correspondence to José D Faraldo-Gómez or David M Mueller.

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Symersky, J., Pagadala, V., Osowski, D. et al. Structure of the c10 ring of the yeast mitochondrial ATP synthase in the open conformation. Nat Struct Mol Biol 19, 485–491 (2012). https://doi.org/10.1038/nsmb.2284

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