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The crystal structure of dynamin

Nature volume 477, pages 561–566 (2011)Cite this article

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Abstract

Dynamin-related proteins (DRPs) are multi-domain GTPases that function via oligomerization and GTP-dependent conformational changes to play central roles in regulating membrane structure across phylogenetic kingdoms. How DRPs harness self-assembly and GTP-dependent conformational changes to remodel membranes is not understood. Here we present the crystal structure of an assembly-deficient mammalian endocytic DRP, dynamin 1, lacking the proline-rich domain, in its nucleotide-free state. The dynamin 1 monomer is an extended structure with the GTPase domain and bundle signalling element positioned on top of a long helical stalk with the pleckstrin homology domain flexibly attached on its opposing end. Dynamin 1 dimer and higher order dimer multimers form via interfaces located in the stalk. Analysis of these interfaces provides insight into DRP family member specificity and regulation and provides a framework for understanding the biogenesis of higher order DRP structures and the mechanism of DRP-mediated membrane scission events.

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Figure 1: The G397D mutation in Dyn1 ΔPRD blocks self-assembly.
Figure 2: The crystal structure of Dyn1 G397D ΔPRD.
Figure 3: Dyn1 G397D ΔPRD stalk interfaces mediate self-assembly.
Figure 4: Oligomerization of dynamin into helical structures.
Figure 5: Model for dynamin GTP cycle conformational changes.

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Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for Dyn1 G397D DPRD have been deposited with the Protein Data Bank under accession code 3ZVR.

References

  1. Praefcke, G. J. & McMahon, H. T. The dynamin superfamily: universal membrane tubulation and fission molecules? Nature Rev. Mol. Cell Biol. 5, 133–147 (2004)

    Article  CAS  Google Scholar 

  2. Hoppins, S., Lackner, L. & Nunnari, J. The machines that divide and fuse mitochondria. Annu. Rev. Biochem. 76, 751–780 (2007)

    Article  CAS  Google Scholar 

  3. Marks, B. et al. GTPase activity of dynamin and resulting conformation change are essential for endocytosis. Nature 410, 231–235 (2001)

    Article  ADS  CAS  Google Scholar 

  4. Stowell, M. H. B., Marks, B., Wigge, P. & McMahon, H. T. Nucleotide-dependent conformational changes in dynamin: evidence for a mechanochemical molecular spring. Nature Cell Biol. 1, 27–32 (1999)

    Article  CAS  Google Scholar 

  5. Mears, J. A. et al. Conformational changes in Dnm1 support a contractile mechanism for mitochondrial fission. Nature Struct. Mol. Biol. 18, 20–26 (2011)

    Article  CAS  Google Scholar 

  6. Warnock, D. E., Hinshaw, J. E. & Schmid, S. L. Dynamin self-assembly stimulates its GTPase activity. J. Biol. Chem. 271, 22310–22314 (1996)

    Article  CAS  Google Scholar 

  7. Danino, D., Moon, K. H. & Hinshaw, J. E. Rapid constriction of lipid bilayers by the mechanochemical enzyme dynamin. J. Struct. Biol. 147, 259–267 (2004)

    Article  CAS  Google Scholar 

  8. Pucadyil, T. J. & Schmid, S. L. Real-time visualization of dynamin-catalyzed membrane fission and vesicle release. Cell 135, 1263–1275 (2008)

    Article  CAS  Google Scholar 

  9. Chappie, J. S. et al. An intramolecular signaling element that modulates dynamin function in vitro and in vivo . Mol. Biol. Cell 20, 3561–3571 (2009)

    Article  CAS  Google Scholar 

  10. Chappie, J. S., Acharya, S., Leonard, M., Schmid, S. L. & Dyda, F. G domain dimerization controls dynamin’s assembly-stimulated GTPase activity. Nature 465, 435–440 (2010)

    Article  ADS  CAS  Google Scholar 

  11. Timm, D. et al. Crystal structure of the pleckstrin homology domain from dynamin. Nature Struct. Biol. 1, 782–788 (1994)

    Article  CAS  Google Scholar 

  12. Achiriloaie, M., Barylko, B. & Albanesi, J. P. Essential role of the dynamin pleckstrin homology domain in receptor-mediated endocytosis. Mol. Cell. Biol. 19, 1410–1415 (1999)

    Article  CAS  Google Scholar 

  13. Ferguson, K. M., Lemmon, M. A., Schlessinger, J. & Sigler, P. B. Crystal structure at 2.2 Å resolution of the pleckstrin homology domain from human dynamin. Cell 79, 199–209 (1994)

    Article  CAS  Google Scholar 

  14. Ramachandran, R. et al. Membrane insertion of the pleckstrin homology domain variable loop 1 is critical for dynamin-catalyzed vesicle scission. Mol. Biol. Cell 20, 4630–4639 (2009)

    Article  CAS  Google Scholar 

  15. Hinshaw, J. E. & Schmid, S. L. Dynamin self-assembles into rings suggesting a mechanism for coated vesicle budding. Nature 374, 190–192 (1995)

    Article  ADS  CAS  Google Scholar 

  16. Ingerman, E. et al. Dnm1 forms spirals that are structurally tailored to fit mitochondria. J. Cell Biol. 170, 1021–1027 (2005)

    Article  CAS  Google Scholar 

  17. Mears, J. A., Ray, P. & Hinshaw, J. E. A corkscrew model for dynamin constriction. Structure 15, 1190–1202 (2007)

    Article  CAS  Google Scholar 

  18. Gao, S. et al. Structural basis of oligomerization in the stalk region of dynamin-like MxA. Nature 465, 502–506 (2010)

    Article  ADS  CAS  Google Scholar 

  19. Low, H. H., Sachse, C., Amos, L. A. & Lowe, J. Structure of a bacterial dynamin-like protein lipid tube provides a mechanism for assembly and membrane curving. Cell 139, 1342–1352 (2009)

    Article  Google Scholar 

  20. Low, H. H. & Lowe, J. A bacterial dynamin-like protein. Nature 444, 766–769 (2006)

    Article  ADS  CAS  Google Scholar 

  21. Prakash, B., Praefcke, G. J., Renault, L., Wittinghofer, A. & Herrmann, C. Structure of human guanylate-binding protein 1 representing a unique class of GTP-binding proteins. Nature 403, 567–571 (2000)

    Article  ADS  CAS  Google Scholar 

  22. Ghosh, A., Praefcke, G. J., Renault, L., Wittinghofer, A. & Herrmann, C. How guanylate-binding proteins achieve assembly-stimulated processive cleavage of GTP to GMP. Nature 440, 101–104 (2006)

    Article  ADS  CAS  Google Scholar 

  23. Bian, X. et al. Structures of the atlastin GTPase provide insight into homotypic fusion of endoplasmic reticulum membranes. Proc. Natl Acad. Sci. USA 108, 3976–3981 (2011)

    Article  ADS  CAS  Google Scholar 

  24. Byrnes, L. J. & Sondermann, H. Structural basis for the nucleotide-dependent dimerization of the large G protein atlastin-1/SPG3A. Proc. Natl Acad. Sci. USA 108, 2216–2221 (2011)

    Article  ADS  CAS  Google Scholar 

  25. Zhang, P. & Hinshaw, J. E. Three-dimensional reconstruction of dynamin in the constricted state. Nature Cell Biol. 3, 922–926 (2001)

    Article  CAS  Google Scholar 

  26. Siegel, L. M. & Monty, K. J. Determination of molecular weights and frictional ratios of proteins in impure systems by use of gel filtration and density gradient centrifugation. Application to crude preparations of sulfite and hydroxylamine reductases. Biochim. Biophys. Acta 112, 346–362 (1966)

    Article  CAS  Google Scholar 

  27. Ramachandran, R. et al. The dynamin middle domain is critical for tetramerization and higher-order self-assembly. EMBO J. 26, 559–566 (2007)

    Article  CAS  Google Scholar 

  28. Gao, S. et al. Structural basis of oligomerization in the stalk region of dynamin-like MxA. Nature 465, 502–506 (2010)

    Article  ADS  CAS  Google Scholar 

  29. Song, B. D., Yarar, D. & Schmid, S. L. An assembly-incompetent mutant establishes a requirement for dynamin self-assembly in clathrin-mediated endocytosis in vivo . Mol. Biol. Cell 15, 2243–2252 (2004)

    Article  CAS  Google Scholar 

  30. Reubold, T. F. et al. Crystal structure of the GTPase domain of rat dynamin 1. Proc. Natl Acad. Sci. USA 102, 13093–13098 (2005)

    Article  ADS  CAS  Google Scholar 

  31. Sweitzer, S. M. & Hinshaw, J. E. Dynamin undergoes a GTP-dependent conformational change causing vesiculation. Cell 93, 1021–1029 (1998)

    Article  CAS  Google Scholar 

  32. Bashkirov, P. V. et al. GTPase cycle of dynamin is coupled to membrane squeeze and release, leading to spontaneous fission. Cell 135, 1276–1286 (2008)

    Article  CAS  Google Scholar 

  33. Kenniston, J. A. & Lemmon, M. A. Dynamin GTPase regulation is altered by PH domain mutations found in centronuclear myopathy patients. EMBO J. 29, 3054–3067 (2010)

    Article  CAS  Google Scholar 

  34. Niemann, H. H., Knetsch, M. L., Scherer, A., Manstein, D. J. & Kull, F. J. Crystal structure of a dynamin GTPase domain in both nucleotide-free and GDP-bound forms. EMBO J. 20, 5813–5821 (2001)

    Article  CAS  Google Scholar 

  35. Barylko, B. et al. The proline/arginine-rich domain is a major determinant of dynamin self-activation. Biochemistry 49, 10592–10594 (2010)

    Article  CAS  Google Scholar 

  36. Vallis, Y., Wigge, P., Marks, B., Evans, P. R. & McMahon, H. T. Importance of the pleckstrin homology domain of dynamin in clathrin-mediated endocytosis. Curr. Biol. 9, 257–263 (1999)

    Article  CAS  Google Scholar 

  37. Durieux, A. C., Prudhon, B., Guicheney, P. & Bitoun, M. Dynamin 2 and human diseases. J. Mol. Med. 88, 339–350 (2010)

    Article  Google Scholar 

  38. Lackner, L. L., Horner, J. S. & Nunnari, J. Mechanistic analysis of a dynamin effector. Science 325, 874–877 (2009)

    Article  ADS  CAS  Google Scholar 

  39. Gandre-Babbe, S. & van der Bliek, A. M. The novel tail-anchored membrane protein Mff controls mitochondrial and peroxisomal fission in mammalian cells. Mol. Biol. Cell 19, 2402–2412 (2008)

    Article  CAS  Google Scholar 

  40. Kosaka, T. & Ikeda, K. Possible temperature-dependent blockage of synaptic vesicle recycling induced by a single gene mutation in Drosophila . J. Neurobiol. 14, 207–225 (1983)

    Article  CAS  Google Scholar 

  41. Ramaswami, M., Rao, S., van der Bliek, A., Kelly, R. B. & Krishnan, K. S. Genetic studies on dynamin function in Drosophila . J. Neurogenet. 9, 73–87 (1993)

    Article  CAS  Google Scholar 

  42. Narayanan, R., Leonard, M., Song, B. D., Schmid, S. L. & Ramaswami, M. An internal GAP domain negatively regulates presynaptic dynamin in vivo: a two-step model for dynamin function. J. Cell Biol. 169, 117–126 (2005)

    Article  CAS  Google Scholar 

  43. Ingerman, E. & Nunnari, J. A continuous, regenerative coupled GTPase assay for dynamin-related proteins. Methods Enzymol. 404, 611–619 (2005)

    Article  CAS  Google Scholar 

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Acknowledgements

The authors would like to express thanks to I. Stokes-Rees for assistance with the Wide Space Molecular Replacement, J. Holton for advice and assistance with data collection and H. McMahon for the kind gift of the dynamin clone. We would also like to thank J. Al-Bassam, J. Chappie, A. McCoy, S. Harrison, D. Owen, A. Fisher, E. Baldwin, L. Lackner, G. Adamson, N. Varlakhanova and members of the Nunnari lab for extensive discussions. S.J. is a Damon Runyon Cancer Research Foundation Fellow supported by the Howard Hughes Medical Institute (DRG-2004-09). This work was supported by an American Heart Innovator Award and NIH grants (R01GM062942S1 and R01GM097432) to J.N. The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the US Department of Energy under Contract No. DE-AC02-05CH11231.

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Authors and Affiliations

  1. Department of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616, USA,

    Marijn G. J. Ford & Jodi Nunnari

  2. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, 02115, Massachusetts, USA

    Simon Jenni

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Contributions

M.G.J.F. purified, biochemically characterized and crystallized the Dyn1 G397D ΔPRD. M.G.J.F. collected X-ray diffraction data and M.G.J.F. and S.J. solved the structure. M.G.J.F. and J.N. designed experiments and M.G.J.F., S.J. and J.N. interpreted data and prepared the manuscript.

Corresponding author

Correspondence to Jodi Nunnari.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

The file contains Supplementary Figures 1-5 with legends, Supplementary Methods, Supplementary Tables 1-3 and Supplementary References. This file was corrected on 07 October 2011 to change the Protein names from rDyn1 to Dyn1 and Dynamin-1 to Dynamin respectively. (PDF 2774 kb)

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Ford, M., Jenni, S. & Nunnari, J. The crystal structure of dynamin. Nature 477, 561–566 (2011). https://doi.org/10.1038/nature10441

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