Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Coordinated conformational changes in the V1 complex during V-ATPase reversible dissociation

Abstract

Vacuolar-type ATPases (V-ATPases) are rotary enzymes that acidify intracellular compartments in eukaryotic cells. These multi-subunit complexes consist of a cytoplasmic V1 region that hydrolyzes ATP and a membrane-embedded VO region that transports protons. V-ATPase activity is regulated by reversible dissociation of the two regions, with the isolated V1 and VO complexes becoming autoinhibited on disassembly and subunit C subsequently detaching from V1. In yeast, assembly of the V1 and VO regions is mediated by the regulator of the ATPase of vacuoles and endosomes (RAVE) complex through an unknown mechanism. We used cryogenic-electron microscopy of yeast V-ATPase to determine structures of the intact enzyme, the dissociated but complete V1 complex and the V1 complex lacking subunit C. On separation, V1 undergoes a dramatic conformational rearrangement, with its rotational state becoming incompatible for reassembly with VO. Loss of subunit C allows V1 to match the rotational state of VO, suggesting how RAVE could reassemble V1 and VO by recruiting subunit C.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Structure of intact yeast V-ATPase.
Fig. 2: Structure of the complete V1 complex.
Fig. 3: Structures of the V1ΔC complex in three rotational states.
Fig. 4: Cycle of conformational changes in V-ATPase reversible dissociation.

Similar content being viewed by others

Data availability

The cryo-EM maps and model coordinates have been deposited to the Electron Microscopy Data Bank (EMDB) (codes EMD-25996 to EMD-26002) and PDB (codes 7TMM, 7TMO, 7TMP, 7TMQ, 7TMR, 7TMS and 7TMT), respectively. Yeast strains and plasmids are available from the corresponding author. Starting models for the construction of atomic models came from the PDB (codes 3J9T, 1HO8, 1U7L and 6M0R). Source data are provided with this paper.

References

  1. Forgac, M. Vacuolar ATPases: rotary proton pumps in physiology and pathophysiology. Nat. Rev. Mol. Cell Biol. 8, 917–929 (2007).

    Article  CAS  PubMed  Google Scholar 

  2. Vasanthakumar, T. & Rubinstein, J. L. Structure and roles of V-type ATPases. Trends Biochem. Sci. 45, 295–307 (2020).

    Article  CAS  PubMed  Google Scholar 

  3. Qin, A. et al. V-ATPases in osteoclasts: structure, function and potential inhibitors of bone resorption. Int. J. Biochem. Cell Biol. 44, 1422–1435 (2012).

    Article  CAS  PubMed  Google Scholar 

  4. Brown, D., Paunescu, T. G., Breton, S. & Marshansky, V. Regulation of the V-ATPase in kidney epithelial cells: dual role in acid–base homeostasis and vesicle trafficking. J. Exp. Biol. 212, 1762–1772 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Stransky, L., Cotter, K. & Forgac, M. The function of V-ATPases in cancer. Physiol. Rev. 96, 1071–1091 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Colacurcio, D. J. & Nixon, R. A. Disorders of lysosomal acidification—the emerging role of v-ATPase in aging and neurodegenerative disease. Ageing Res. Rev. 32, 75–88 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Kornak, U. Mutations in the a3 subunit of the vacuolar H+-ATPase cause infantile malignant osteopetrosis. Hum. Mol. Genet. 9, 2059–2063 (2000).

    Article  CAS  PubMed  Google Scholar 

  8. Karet, F. E. et al. Mutations in the gene encoding B1 subunit of H+-ATPase cause renal tubular acidosis with sensorineural deafness. Nat. Genet. 21, 84–90 (1999).

    Article  CAS  PubMed  Google Scholar 

  9. Zhao, J., Benlekbir, S. & Rubinstein, J. L. Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase. Nature 521, 241–245 (2015).

    Article  CAS  PubMed  Google Scholar 

  10. Mazhab-Jafari, M. T. et al. Atomic model for the membrane-embedded VO motor of a eukaryotic V-ATPase. Nature 539, 118–122 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Roh, S.-H. et al. The 3.5-Å CryoEM structure of nanodisc-reconstituted yeast vacuolar ATPase Vo proton channel. Mol. Cell 69, 993–1004.e3 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Abbas, Y. M., Wu, D., Bueler, S. A., Robinson, C. V. & Rubinstein, J. L. Structure of V-ATPase from the mammalian brain. Science 367, 1240–1246 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Moriyama, Y., Maeda, M. & Futai, M. The role of V-ATPase in neuronal and endocrine systems. J. Exp. Biol. 172, 171–178 (1992).

    Article  CAS  PubMed  Google Scholar 

  14. Kane, P. M. Disassembly and reassembly of the yeast vacuolar H+-ATPase in vivo. J. Biol. Chem. 270, 17025–17032 (1995).

    Article  CAS  PubMed  Google Scholar 

  15. Sumner, J. P. et al. Regulation of plasma membrane V-ATPase activity by dissociation of peripheral subunits. J. Biol. Chem. 270, 5649–5653 (1995).

    Article  CAS  PubMed  Google Scholar 

  16. Trombetta, E. S., Ebersold, M., Garrett, W., Pypaert, M. & Mellman, I. Activation of lysosomal function during dendritic cell maturation. Science 299, 1400–1403 (2003).

    Article  CAS  PubMed  Google Scholar 

  17. Sautin, Y. Y., Lu, M., Gaugler, A., Zhang, L. & Gluck, S. L. Phosphatidylinositol 3-kinase-mediated effects of glucose on vacuolar H+-ATPase assembly, translocation, and acidification of intracellular compartments in renal epithelial cells. Mol. Cell Biol. 25, 15 (2005).

    Article  CAS  Google Scholar 

  18. Stransky, L. A. & Forgac, M. Amino acid availability modulates vacuolar H+-ATPase assembly. J. Biol. Chem. 290, 27360–27369 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Bodzęta, A., Kahms, M. & Klingauf, J. The presynaptic v-ATPase reversibly disassembles and thereby modulates exocytosis but is not part of the fusion machinery. Cell Rep. 20, 1348–1359 (2017).

    Article  PubMed  CAS  Google Scholar 

  20. Poëa-Guyon, S. et al. The V-ATPase membrane domain is a sensor of granular pH that controls the exocytotic machinery. J. Cell Biol. 203, 283–298 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  21. Li, S. C., Diakov, T. T., Rizzo, J. M. & Kane, P. M. Vacuolar H+-ATPase works in parallel with the HOG pathway to adapt Saccharomyces cerevisiae cells to osmotic stress. Eukaryot. Cell 11, 282–291 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Diakov, T. T. & Kane, P. M. Regulation of vacuolar proton-translocating ATPase activity and assembly by extracellular pH. J. Biol. Chem. 285, 23771–23778 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Zhang, Z., Charsky, C., Kane, P. M. & Wilkens, S. Yeast V1-ATPase. J. Biol. Chem. 278, 47299–47306 (2003).

    Article  CAS  PubMed  Google Scholar 

  24. Hildenbrand, Z. L., Molugu, S. K., Stock, D. & Bernal, R. A. The C-H peripheral stalk base: a novel component in V1-ATPase assembly. PLoS ONE 5, e12588 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  25. Diab, H., Ohira, M., Liu, M., Cobb, E. & Kane, P. M. Subunit interactions and requirements for inhibition of the yeast V1-ATPase. J. Biol. Chem. 284, 13316–13325 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Parra, K. J., Keenan, K. L. & Kane, P. M. The H Subunit (Vma13p) of the yeast V-ATPase inhibits the ATPase activity of cytosolic V1 complexes. J. Biol. Chem. 275, 21761–21767 (2000).

    Article  CAS  PubMed  Google Scholar 

  27. Couoh-Cardel, S., Milgrom, E. & Wilkens, S. Affinity purification and structural features of the yeast vacuolar ATPase Vo membrane sector. J. Biol. Chem. 290, 27959–27971 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Benlekbir, S., Bueler, S. A. & Rubinstein, J. L. Structure of the vacuolar-type ATPase from Saccharomyces cerevisiae at 11-Å resolution. Nat. Struct. Mol. Biol. 19, 1356–1362 (2012).

    Article  CAS  PubMed  Google Scholar 

  29. Sagermann, M., Stevens, T. H. & Matthews, B. W. Crystal structure of the regulatory subunit H of the V-type ATPase of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 98, 7134–7139 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Oot, R. A., Kane, P. M., Berry, E. A. & Wilkens, S. Crystal structure of yeast V1ATP ase in the autoinhibited state. EMBO J. 35, 1694–1706 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Sharma, S., Oot, R. A., Khan, M. M. & Wilkens, S. Functional reconstitution of vacuolar H+-ATPase from Vo proton channel and mutant V1-ATPase provides insight into the mechanism of reversible disassembly. J. Biol. Chem. 294, 6439–6449 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Seol, J. H., Shevchenko, A., Shevchenko, A. & Deshaies, R. J. Skp1 forms multiple protein complexes, including RAVE, a regulator of V-ATPase assembly. Nat. Cell Biol. 3, 384–391 (2001).

    Article  CAS  PubMed  Google Scholar 

  33. Smardon, A. M., Tarsio, M. & Kane, P. M. The RAVE complex is essential for stable assembly of the yeast V-ATPase. J. Biol. Chem. 277, 13831–13839 (2002).

    Article  CAS  PubMed  Google Scholar 

  34. Einhorn, Z., Trapani, J. G., Liu, Q. & Nicolson, T. Rabconnectin3 promotes stable activity of the H+ pump on synaptic vesicles in hair cells. J. Neurosci. 32, 11144–11156 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Yan, Y., Denef, N. & Schüpbach, T. The vacuolar proton pump, V-ATPase, is required for notch signaling and endosomal trafficking in Drosophila. Dev. Cell 17, 387–402 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Smardon, A. M., Nasab, N. D., Tarsio, M., Diakov, T. T. & Kane, P. M. Molecular interactions and cellular itinerary of the yeast RAVE (Regulator of the H+-ATPase of Vacuolar and Endosomal Membranes) complex. J. Biol. Chem. 290, 27511–27523 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Jaskolka, M. C., Tarsio, M., Smardon, A. M., Khan, Md. M. & Kane, P. M. Defining steps in RAVE-catalyzed V-ATPase assembly using purified RAVE and V-ATPase subcomplexes. J. Biol. Chem. 296, 100703 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Wang, R. et al. Cryo-EM structures of intact V-ATPase from bovine brain. Nat. Commun. 11, 3921 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Wang, L., Wu, D., Robinson, C. V., Wu, H. & Fu, T.-M. Structures of a complete human V-ATPase reveal mechanisms of its assembly. Mol. Cell 80, 501–511.e3 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).

    Article  CAS  PubMed  Google Scholar 

  41. Guo, H. et al. Structure of mycobacterial ATP synthase bound to the tuberculosis drug bedaquiline. Nature 589, 143–147 (2021).

    Article  CAS  PubMed  Google Scholar 

  42. Punjani, A. & Fleet, D. J. 3D variability analysis: resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM. J. Struct. Biol. 213, 107702 (2021).

    Article  CAS  PubMed  Google Scholar 

  43. Muench, S. P. et al. Subunit positioning and stator filament stiffness in regulation and power transmission in the V1 motor of the Manduca sexta V-ATPase. J. Mol. Biol. 426, 286–300 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Jefferies, K. C. & Forgac, M. Subunit H of the vacuolar (H+) ATPase inhibits ATP hydrolysis by the free V1 domain by interaction with the rotary subunit F. J. Biol. Chem. 283, 4512–4519 (2008).

    Article  CAS  PubMed  Google Scholar 

  45. Zhao, J. et al. Molecular basis for the binding and modulation of V-ATPase by a bacterial effector protein. PLoS Pathog. 13, e1006394 (2017).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  46. Sambade, M., Alba, M., Smardon, A. M., West, R. W. & Kane, P. M. A genomic screen for yeast vacuolar membrane ATPase mutants. Genetics 170, 1539–1551 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Voss, M., Vitavska, O., Walz, B., Wieczorek, H. & Baumann, O. Stimulus-induced phosphorylation of vacuolar H+-ATPase by protein kinase A*. J. Biol. Chem. 282, 33735–33742 (2007).

    Article  CAS  PubMed  Google Scholar 

  48. Hong-Hermesdorf, A., Brüx, A., Grüber, A., Grüber, G. & Schumacher, K. A WNK kinase binds and phosphorylates V-ATPase subunit C. FEBS Lett. 580, 932–939 (2006).

    Article  CAS  PubMed  Google Scholar 

  49. Tabke, K. et al. Reversible disassembly of the yeast V-ATPase revisited under in vivo conditions. Biochem. J. 462, 185–197 (2014).

    Article  CAS  PubMed  Google Scholar 

  50. Banerjee, S. & Kane, P. M. Direct interaction of the Golgi V-ATPase a-subunit isoform with PI(4)P drives localization of Golgi V-ATPases in yeast. Mol. Biol. Cell 28, 2518–2530 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Banerjee, S., Clapp, K., Tarsio, M. & Kane, P. M. Interaction of the late endo-lysosomal lipid PI(3,5)P2 with the Vph1 isoform of yeast V-ATPase increases its activity and cellular stress tolerance. J. Biol. Chem. 294, 9161–9171 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Vasanthakumar, T. et al. Structural comparison of the vacuolar and Golgi V-ATPases from Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 116, 7272–7277 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Marr, C. R., Benlekbir, S. & Rubinstein, J. L. Fabrication of carbon films with 500 nm holes for cryo-EM with a direct detector device. J. Struct. Biol. 185, 42–47 (2014).

    Article  CAS  PubMed  Google Scholar 

  54. Tivol, W. F., Briegel, A. & Jensen, G. J. An improved cryogen for plunge freezing. Microsc. Microanal. 14, 375–379 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Punjani, A. Algorithmic advances in single particle cryo-EM data processing using CryoSPARC. Microsc. Microanal. 26, 2322–2323 (2020).

    Article  Google Scholar 

  56. Rubinstein, J. L. & Brubaker, M. A. Alignment of cryo-EM movies of individual particles by optimization of image translations. J. Struct. Biol. 192, 1–11 (2015).

    Article  Google Scholar 

  57. Punjani, A., Zhang, H. & Fleet, D. J. Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction. Nat. Methods 17, 1214–1221 (2020).

    Article  CAS  PubMed  Google Scholar 

  58. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D. Biol. Crystallogr. 60, 2126–2132 (2004).

    Article  PubMed  CAS  Google Scholar 

  59. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D. Biol. Crystallogr. 66, 213–221 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. Sect. Struct. Biol. 74, 519–530 (2018).

    Article  CAS  Google Scholar 

  61. Pettersen, E. F. et al. UCSF Chimera? A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

    Article  CAS  PubMed  Google Scholar 

  62. Drory, O., Frolow, F. & Nelson, N. Crystal structure of yeast V‐ATPase subunit C reveals its stator function. EMBO Rep. 5, 1148–1152 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Ashkenazy, H. et al. ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Res. 44, W344–W350 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis: UCSF ChimeraX Visualization System. Protein Sci. 27, 14–25 (2018).

    Article  CAS  PubMed  Google Scholar 

  65. Kornberg, A. & Pricer, W. E. Enzymatic phosphorylation of adenosine and 2,6-diaminopurine riboside. J. Biol. Chem. 193, 481–496 (1951).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank S. Benlekbir, Y. Z. Tan and H. Guo (The Hospital for Sick Children) for assistance with cryo-EM data collection. We thank P. Kane (SUNY Upstate Medical University) for the gift of the PMK549 yeast strain and for discussions about yeast growth, and S. Wilkens and R. Oot for discussions about the V1∆C crystal structure. T.V. was supported by an Ontario Graduate Scholarship, K.A.K. was supported by an Ontario Graduate Scholarship and a Canada Graduate Scholarship and J.L.R. was supported by the Canada Research Chairs program. This work was supported by Canadian Institutes of Health Research grant no. PJT166152 (J.L.R.). Cryo-EM data were collected at the Toronto High-Resolution High-Throughput cryo-EM facility and enzyme assays performed using infrastructure from the Hospital for Sick Children’s Structural and Biophysical Core Facility, both of which are supported by the Canada Foundation for Innovation and Ontario Research Fund. Mass spectrometry data were collected at the Network Biology Collaborative Center at the Lunenfeld-Tanenbaum Research Institute.

Author information

Authors and Affiliations

Authors

Contributions

T.V. purified V1, V1∆C, V1∆H and recombinant subunit H constructs, and performed enzyme assays, cryo-EM and the analysis associated with those specimens. K.A.K. purified intact V-ATPase and performed the cryo-EM and analysis for that specimen. S.A.B. prepared the VMA1-3×FLAG, vma5∆ yeast strain. M.C.J. prepared protein for early experiments and advised on protein purification. J.L.R. supervised and coordinated experiments. T.V. and J.L.R. wrote the manuscript and prepared figures with input from the other authors.

Corresponding author

Correspondence to John L. Rubinstein.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Structural & Molecular Biology thanks Stephen Muench and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available. Primary Handling Editor: Florian Ullrich, in collaboration with the Nature Structural & Molecular Biology team.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 CryoEM of intact V-ATPase.

a, Example micrograph (from a dataset of 4015 micrographs) and 2D class average images. b, Fourier shell correlation curves after gold-standard refinement and correction for masking for the three rotational states of intact V-ATPase. c, Local resolution maps and orientation distribution plots for rotational State 1 (top), State 2 (middle), and State 3 (bottom). d, Masks (light blue density) used for local refinement of the V1 region (top), subunit a and the collar region (middle), and the VO region (bottom) for V-ATPase (shown for State 1).

Extended Data Fig. 2 CryoEM of the complete V1 complex.

a, Example micrograph (from a dataset of 3212 micrographs) and 2D class average images. b, Fourier shell correlation curves after gold-standard refinement and correction for masking for the complete V1 complex and V1∆C from the complete V1 protein preparation. c, Local resolution maps and orientation distribution plot for complete V1. d, Local resolution maps and orientation distribution plot for V1∆C in State 3.

Extended Data Fig. 3 Interface between subunit C and the central rotor in complete V1.

Subunit C (colored by sequence conservation) rotates toward the central rotor subunits F and D (gray) upon dissociation of V1 from VO. There is minimal sequence conservation on the surface of subunit C that interacts with the central rotor in the complete V1 complex. However, in the complete V1 complex subunit C is positioned to block rotation of the rotor subcomplex and prevent rotation from State 2 to State 3.

Extended Data Fig. 4 CryoEM of the V1ΔC complex.

a, Example micrograph (from a dataset of 11,175 micrographs), 2D class average images, and Fourier shell correlation curves after gold-standard refinement and correction for masking for V1∆C in States 2 and 3. b, Example micrograph (from a dataset of 4277 micrographs), 2D class average images, and Fourier shell correlation curves after gold standard refinement and correction for masking for V1∆C with 1 mM ATP in States 1, 2, and 3. c, Local resolution maps and orientation distribution plot for V1∆C in State 2 (top) and State 3 (bottom). d, Local resolution maps and orientation distribution plot for V1∆C with 1 mM ATP in State 1 (top), State 2 (middle), and State 3 (bottom).

Extended Data Fig. 5 Additional structure of V1ΔC complex that appears when the protein preparation is left at 4 °C.

a, CryoEM of the V1∆C sample showed an additional structure that increased in abundance the longer the sample was left at 4 °C. b, The additional structure fits the model of the V1∆C complex from X-ray crystallography30 (orange) along with an additional peripheral stalk and subunit H from an adjacent V1∆C complex in the crystal lattice (blue). c, The entire map of the additional structure is explained by V1∆C from the crystal (orange), an adjacent subunit H and peripheral stalk from the crystal (blue), and a third subunit H (red) not found in the crystal, but matching the conformation of subunit H observed in the cryo-EM maps. d, Replication of the assay results shown in Fig. 3b with separately purified batches of protein. V1ΔH (pink circles) has strong ATPase activity with a 5-fold excess of recombinant wildtype subunit H (green squares) inhibiting activity but a 5-fold excess of recombinant subunit H bearing the mutation I473D (blue triangles) unable to inhibit (mean ± s.d., n = 3 assays). Data for the graph in D are available as source data.

Source data

Supplementary information

Reporting Summary

Peer Review File

Supplementary Video 1

Three-dimensional variability analysis shows flexibility in the collar region of the complete V1 complex.

Supplementary Video 2

Interpolation between the structure of V1 within intact V-ATPase and in the complete V1 complex shows the conformational changes that occur in V1 on separation from VO.

Supplementary Video 3

Three-dimensional variability analysis shows flexibility in subunit H and the peripheral stalks of the V1ΔC complex in all three rotational states.

Supplementary Video 4

Model for the conformational changes that occur during the cycle of dissociation and reassembly of the V1 and VO complexes.

Source data

Source Data Fig. 1

Unprocessed gel.

Source Data Fig. 2

Unprocessed gel.

Source Data Fig. 3

Unprocessed gel.

Source Data Fig. 3

Summary of mass spectrometry data for the bands identified in Fig. 3a.

Source Data Fig. 3

Source data for ATPase assays shown in Fig. 3b.

Source Data Extended Data Fig. 5

Source data for ATPase assays.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Vasanthakumar, T., Keon, K.A., Bueler, S.A. et al. Coordinated conformational changes in the V1 complex during V-ATPase reversible dissociation. Nat Struct Mol Biol 29, 430–439 (2022). https://doi.org/10.1038/s41594-022-00757-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41594-022-00757-z

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing