Crossref journal-article
eLife Sciences Publications, Ltd
eLife (4374)
Abstract

Adenosine triphosphate (ATP), the chemical energy currency of biology, is synthesized in eukaryotic cells primarily by the mitochondrial ATP synthase. ATP synthases operate by a rotary catalytic mechanism where proton translocation through the membrane-inserted FO region is coupled to ATP synthesis in the catalytic F1 region via rotation of a central rotor subcomplex. We report here single particle electron cryomicroscopy (cryo-EM) analysis of the bovine mitochondrial ATP synthase. Combining cryo-EM data with bioinformatic analysis allowed us to determine the fold of the a subunit, suggesting a proton translocation path through the FO region that involves both the a and b subunits. 3D classification of images revealed seven distinct states of the enzyme that show different modes of bending and twisting in the intact ATP synthase. Rotational fluctuations of the c8-ring within the FO region support a Brownian ratchet mechanism for proton-translocation-driven rotation in ATP synthases.

Bibliography

Zhou, A., Rohou, A., Schep, D. G., Bason, J. V., Montgomery, M. G., Walker, J. E., Grigorieff, N., & Rubinstein, J. L. (2015). Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM. ELife, 4. CLOCKSS.

Authors 8
  1. Anna Zhou (first)
  2. Alexis Rohou (additional)
  3. Daniel G Schep (additional)
  4. John V Bason (additional)
  5. Martin G Montgomery (additional)
  6. John E Walker (additional)
  7. Nikolaus Grigorieff (additional)
  8. John L Rubinstein (additional)
References 55 Referenced 263
  1. 10.1038/nature14185 / Nature / Horizontal membrane-intrinsic α-helices in the stator a-subunit of an F-type ATP synthase by Allegretti (2015)
  2. 10.1016/j.jsb.2009.11.014 / Journal of Structural Biology / The resolution dependence of optimal exposures in liquid nitrogen temperature electron cryomicroscopy of catalase crystals by Baker (2010)
  3. 10.1073/pnas.1204935109 / Proceedings of the National Academy of Sciences of the United States of America / Arrangement of subunits in intact mammalian mitochondrial ATP synthase determined by cryo-EM by Baker (2012)
  4. 10.1074/jbc.271.34.20340 / The Journal of Biological Chemistry / Membrane topography and near-neighbor relationships of the mitochondrial ATP synthase subunits e, f, and g* by Belogrudov (1996)
  5. 10.1146/annurev.biochem.66.1.717 / Annual Review of Biochemistry / The ATP synthase--a splendid molecular machine by Boyer (1997)
  6. 10.1016/j.ab.2009.08.006 / Analytical Biochemistry / Measurement of the molecular masses of hydrophilic and hydrophobic subunits of ATP synthase and complex I in a single experiment by Carroll (2009)
  7. 10.1016/j.febslet.2007.05.079 / FEBS Letters / Association of two proteolipids of unknown function with ATP synthase from bovine heart mitochondria by Chen (2007)
  8. 10.1093/protein/6.1.59 / Protein Engineering / Modeling of transmembrane seven helix bundles by Cronet (1993)
  9. 10.1073/pnas.1103621108 / Proceedings of the National Academy of Sciences of the United States of America / Macromolecular organization of ATP synthase and complex I in whole mitochondria by Davies (2011)
  10. 10.1038/sj.emboj.7601177 / The EMBO Journal / On the structure of the stator of the mitochondrial ATP synthase by Dickson (2006)
  11. 10.1016/j.jmb.2009.07.008 / Journal of Molecular Biology / Refinement of protein structures into low-resolution density maps using rosetta by Dimaio (2009)
  12. 10.1002/0471250953.bi0506s15 / Current Protocols in Bioinformatics by Eswar (2006)
  13. 10.1002/j.1460-2075.1986.tb04456.x / The EMBO Journal / Two overlapping genes in bovine mitochondrial DNA encode membrane components of ATP synthase by Fearnley (1986)
  14. 10.1073/pnas.0707326104 / Proceedings of the National Academy of Sciences of the United States of America / How the regulatory protein, IF(1), inhibits F(1)-ATPase from bovine mitochondria by Gledhill (2007)
  15. 10.1016/j.jsb.2006.06.010 / Journal of Structural Biology / Visualizing density maps with UCSF chimera by Goddard (2007)
  16. 10.1016/j.jsb.2015.08.006 / Journal of Structural Biology / Automatic estimation and correction of anisotropic magnification distortion in electron microscopes by Grant (2015)
  17. 10.7554/eLife.06980.015 / eLife / Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6 by Grant (2015)
  18. 10.1016/j.jsb.2006.05.004 / Journal of Structural Biology / FREALIGN: high-resolution refinement of single particle structures by Grigorieff (2007)
  19. 10.1002/prot.340180402 / Proteins / Correlated mutations and residue contacts in proteins by Göbel (1994)
  20. 10.1016/j.cell.2012.04.012 / Cell / Three-dimensional structures of membrane proteins from genomic sequencing by Hopf (2012)
  21. 10.1146/annurev.biochem.75.062003.101730 / Annual Review of Biochemistry / Energy transduction: proton transfer through the respiratory complexes by Hosler (2006)
  22. 10.7554/eLife.06119 / eLife / Bovine F1F0 ATP synthase monomers bend the lipid bilayer in 2D membrane crystals by Jiko (2015)
  23. 10.1016/S0968-0004(97)01129-8 / Trends in Biochemical Sciences / ATP synthase: an electrochemical transducer with rotatory mechanics by Junge (1997)
  24. 10.1126/science.1112617 / Science / Structural biology. Nature's rotary electromotors by Junge (2005)
  25. 10.1016/j.jmb.2008.08.014 / Journal of Molecular Biology / Cryo-EM structure of the yeast ATP synthase by Lau (2008)
  26. 10.1038/nature10699 / Nature / Subnanometre-resolution structure of the intact thermus thermophilus H+-driven ATP synthase by Lau (2012)
  27. 10.1016/j.jsb.2013.07.005 / Journal of Structural Biology / Likelihood-based classification of cryo-EM images using FREALIGN by Lyumkis (2013)
  28. 10.1371/journal.pone.0028766.s022 / PloS One / Protein 3D structure computed from evolutionary sequence variation by Marks (2011)
  29. 10.1016/j.jsb.2013.11.002 / Journal of Structural Biology / Fabrication of carbon films with ∼ 500nm holes for cryo-EM with a direct detector device by Marr (2014)
  30. 10.1016/j.jsb.2005.07.007 / Journal of Structural Biology / Automated electron microscope tomography using robust prediction of specimen movements by Mastronarde (2005)
  31. 10.1073/pnas.0503893102 / Proceedings of the National Academy of Sciences of the United States of America / Structure of dimeric mitochondrial ATP synthase: novel F0 bridging features and the structural basis of mitochondrial cristae biogenesis by Minauro-Sanmiguel (2005)
  32. 10.1186/1471-2105-10-159 / BMC Bioinformatics / Transmembrane protein topology prediction using support vector machines by Nugent (2009)
  33. 10.7554/eLife.02030 / eLife / Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information by Ovchinnikov (2014)
  34. 10.1016/j.jsb.2010.03.007 / Journal of Structural Biology / Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions by Pintilie (2010)
  35. 10.1038/nchembio.457 / Nature Chemical Biology / Microscopic rotary mechanism of ion translocation in the F(o) complex of ATP synthases by Pogoryelov (2010)
  36. 10.1038/nsmb.1678 / Nature Structural & Molecular Biology / High-resolution structure of the rotor ring of a proton-dependent ATP synthase by Pogoryelov (2009)
  37. 10.1073/pnas.0910365106 / Proceedings of the National Academy of Sciences of the United States of America / The structure of the membrane extrinsic region of bovine ATP synthase by Rees (2009)
  38. 10.1016/S0076-6879(04)83004-0 / Methods in Enzymology / Protein structure prediction using rosetta by Rohl (2004)
  39. 10.1016/j.jsb.2015.08.008 / Journal of Structural Biology / CTFFIND4: fast and accurate defocus estimation from electron micrographs by Rohou (2015)
  40. 10.1016/j.jsb.2015.08.007 / Journal of Structural Biology / Alignment of cryo-EM movies of individual particles by optimization of image translations by Rubinstein (2015)
  41. 10.1093/emboj/cdg608 / The EMBO Journal / Structure of the mitochondrial ATP synthase by electron cryomicroscopy by Rubinstein (2003)
  42. 10.1098/rsob.120160 / Open Biology / The affinity purification and characterization of ATP synthase complexes from mitochondria by Runswick (2013)
  43. 10.1016/j.jsb.2012.09.006 / Journal of Structural Biology / RELION: implementation of a bayesian approach to cryo-EM structure determination by Scheres (2012)
  44. 10.1016/j.jsb.2014.11.010 / Journal of Structural Biology / Semi-automated selection of cryo-EM particles in RELION-1.3 by Scheres (2015)
  45. 10.1038/emboj.2008.35 / The EMBO Journal / Dimer ribbons of ATP synthase shape the inner mitochondrial membrane by Strauss (2008)
  46. 10.1073/pnas.1207912109 / Proceedings of the National Academy of Sciences of the United States of America / Oligomycin frames a common drug-binding site in the ATP synthase by Symersky (2012)
  47. 10.1016/j.str.2008.03.005 / Structure (London, England : 1993) / Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics by Trabuco (2008)
  48. 10.1016/0022-2836(87)90611-5 / Journal of Molecular Biology / ATP synthase from bovine mitochondria. the characterization and sequence analysis of two membrane-associated sub-units and of the corresponding cDNAs by Walker (1987)
  49. 10.1002/(SICI)1521-3773(19980918)37:17<2308::AID-ANIE2308>3.0.CO;2-W / Angewandte Chemie International Edition / ATP synthesis by rotary catalysis (nobel lecture) by Walker (1998)
  50. 10.1073/pnas.96.9.4735 / Biochemical Society Transactions / The ATP synthase: the understood, the uncertain and the unknown by Walker (2013)
  51. 10.1073/pnas.1011099107 / Proceedings of the National Academy of Sciences of the United States of America / Bioenergetic cost of making an adenosine triphosphate molecule in animal mitochondria by Watt (2010)
  52. 10.1006/jsbi.1998.4080 / Journal of Structural Biology / Situs: a package for docking crystal structures into low-resolution maps from electron microscopy by Wriggers (1999)
  53. 10.1038/nature14365 / Nature / Electron cryomicroscopy observation of rotational states in a eukaryotic v-ATPase by Zhao (2015)
  54. 10.1016/j.jsb.2015.06.014 / Journal of Structural Biology / Description and comparison of algorithms for correcting anisotropic magnification in cryo-EM images by Zhao (2015)
  55. 10.1038/nchem.1868 / Nature Chemistry / Ion mobility-mass spectrometry of a rotary ATPase reveals ATP-induced reduction in conformational flexibility by Zhou (2014)
Dates
Type When
Created 9 years, 10 months ago (Oct. 6, 2015, 7:43 a.m.)
Deposited 1 year, 10 months ago (Oct. 11, 2023, 8:53 p.m.)
Indexed 20 hours, 44 minutes ago (Aug. 20, 2025, 8:30 a.m.)
Issued 9 years, 10 months ago (Oct. 6, 2015)
Published 9 years, 10 months ago (Oct. 6, 2015)
Published Online 9 years, 10 months ago (Oct. 6, 2015)
Funders 6
  1. Canadian Institutes of Health Research 10.13039/501100000024

    Region: Americas

    gov (National government)

    Labels6
    1. Instituts de Recherche en Santé du Canada
    2. Canadian Institutes of Health Research (CIHR)
    3. CIHR_IRSC
    4. Canadian Institutes of Health Research | Ottawa ON
    5. CIHR
    6. IRSC
    Awards1
    1. MOP 81294
  2. Medical Research Council 10.13039/501100000265

    Region: Europe

    gov (National government)

    Labels3
    1. Medical Research Council (United Kingdom)
    2. UK Medical Research Council
    3. MRC
    Awards1
    1. U105663150
  3. Howard Hughes Medical Institute 10.13039/100000011

    Region: Americas

    pri (Research institutes and centers)

    Labels2
    1. Howard Hughes Medical Institute Inc
    2. HHMI
  4. Canada Research Chairs (Chaires de recherche du Canada)
  5. Canadian Institutes of Health Research 10.13039/501100000024

    Region: Americas

    gov (National government)

    Labels6
    1. Instituts de Recherche en Santé du Canada
    2. Canadian Institutes of Health Research (CIHR)
    3. CIHR_IRSC
    4. Canadian Institutes of Health Research | Ottawa ON
    5. CIHR
    6. IRSC
    Awards1
    1. postgraduate scholarship
  6. Natural Sciences and Engineering Research Council of Canada 10.13039/501100000038

    Region: Americas

    gov (National government)

    Labels3
    1. Conseil de Recherches en Sciences Naturelles et en Génie du Canada
    2. NSERC
    3. CRSNG
    Awards1
    1. postgraduate scholarship

@article{Zhou_2015, title={Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM}, volume={4}, ISSN={2050-084X}, url={http://dx.doi.org/10.7554/elife.10180}, DOI={10.7554/elife.10180}, journal={eLife}, publisher={eLife Sciences Publications, Ltd}, author={Zhou, Anna and Rohou, Alexis and Schep, Daniel G and Bason, John V and Montgomery, Martin G and Walker, John E and Grigorieff, Nikolaus and Rubinstein, John L}, year={2015}, month=oct }