Crystal structure of nucleotide-free dynamin

Abstract

Dynamin is a mechanochemical GTPase that oligomerizes around the neck of clathrin-coated pits and catalyses vesicle scission in a GTP-hydrolysis-dependent manner. The molecular details of oligomerization and the mechanism of the mechanochemical coupling are currently unknown. Here we present the crystal structure of human dynamin 1 in the nucleotide-free state with a four-domain architecture comprising the GTPase domain, the bundle signalling element, the stalk and the pleckstrin homology domain. Dynamin 1 oligomerized in the crystals via the stalks, which assemble in a criss-cross fashion. The stalks further interact via conserved surfaces with the pleckstrin homology domain and the bundle signalling element of the neighbouring dynamin molecule. This intricate domain interaction rationalizes a number of disease-related mutations in dynamin 2 and suggests a structural model for the mechanochemical coupling that reconciles previous models of dynamin function.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Structure of nucleotide-free human dynamin 1.
Figure 2: The dynamin 1 dimer.
Figure 3: Stalk interactions with the BSE and PH domain.
Figure 4: Model for dynamin oligomerization and function.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The atomic coordinates of human dynamin1 have been deposited in the Protein Data Bank with accession number 3SNH.

References

  1. 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)

    CAS  Article  Google Scholar 

  2. 2

    van der Bliek, A. M. & Meyerowitz, E. M. Dynamin-like protein encoded by the Drosophila shibire gene associated with vesicular traffic. Nature 351, 411–414 (1991)

    ADS  CAS  Article  Google Scholar 

  3. 3

    Ferguson, S. M. et al. A selective activity-dependent requirement for dynamin 1 in synaptic vesicle endocytosis. Science 316, 570–574 (2007)

    ADS  CAS  Article  Google Scholar 

  4. 4

    Robinson, P. J. et al. Dynamin GTPase regulated by protein kinase C phosphorylation in nerve terminals. Nature 365, 163–166 (1993)

    ADS  CAS  Article  Google Scholar 

  5. 5

    Lu, J. et al. Postsynaptic positioning of endocytic zones and AMPA receptor cycling by physical coupling of dynamin-3 to Homer. Neuron 55, 874–889 (2007)

    CAS  Article  Google Scholar 

  6. 6

    Cook, T. A., Urrutia, R. & McNiven, M. A. Identification of dynamin 2, an isoform ubiquitously expressed in rat tissues. Proc. Natl Acad. Sci. USA 91, 644–648 (1994)

    ADS  CAS  Article  Google Scholar 

  7. 7

    Durieux, A. C. et al. Dynamin 2 and human diseases. J. Mol. Med. 88, 339–350 (2010)

    Article  Google Scholar 

  8. 8

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

    ADS  CAS  Article  Google Scholar 

  9. 9

    Roux, A. et al. GTP-dependent twisting of dynamin implicates constriction and tension in membrane fission. Nature 441, 528–531 (2006)

    ADS  CAS  Article  Google Scholar 

  10. 10

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

    ADS  CAS  Article  Google Scholar 

  11. 11

    Stowell, M. H. B. et al. Nucleotide-dependent conformational changes in dynamin: evidence for a mechanochemical molecular spring. Nature Cell Biol. 1, 27–32 (1999)

    CAS  Article  Google Scholar 

  12. 12

    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)

    CAS  Article  Google Scholar 

  13. 13

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

    CAS  Article  Google Scholar 

  14. 14

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

    CAS  Article  Google Scholar 

  15. 15

    Ferguson, K. M. et al. Crystal structure at 2.2 Å resolution of the pleckstrin homology domain from human dynamin. Cell 79, 199–209 (1994)

    CAS  Article  Google Scholar 

  16. 16

    Niemann, H. H. et al. Crystal structure of a dynamin GTPase domain in both nucleotide-free and GDP-bound forms. EMBO J. 20, 5813–5821 (2001)

    CAS  Article  Google Scholar 

  17. 17

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

    ADS  CAS  Article  Google Scholar 

  18. 18

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

    CAS  Article  Google Scholar 

  19. 19

    Chappie, J. S. et al. G domain dimerization controls dynamin’s assembly-stimulated GTPase activity. Nature 465, 435–440 (2010)

    ADS  CAS  Article  Google Scholar 

  20. 20

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

    ADS  CAS  Article  Google Scholar 

  21. 21

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

    CAS  Article  Google Scholar 

  22. 22

    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)

    CAS  Article  Google Scholar 

  23. 23

    Vallis, Y. et al. Importance of the pleckstrin homology domain of dynamin in clathrin-mediated endocytosis. Curr. Biol. 9, 257–263 (1999)

    CAS  Article  Google Scholar 

  24. 24

    Zheng, J. et al. Identification of the binding site for acidic phospholipids on the pH domain of dynamin: implications for stimulation of GTPase activity. J. Mol. Biol. 255, 14–21 (1996)

    CAS  Article  Google Scholar 

  25. 25

    Salim, K. et al. Distinct specificity in the recognition of phosphoinositides by the pleckstrin homology domains of dynamin and Bruton’s tyrosine kinase. EMBO J. 15, 6241–6250 (1996)

    CAS  Article  Google Scholar 

  26. 26

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

    CAS  Article  Google Scholar 

  27. 27

    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)

    CAS  Article  Google Scholar 

  28. 28

    Kochs, G. et al. Assay and functional analysis of dynamin-like Mx proteins. Methods Enzymol. 404, 632–643 (2005)

    CAS  Article  Google Scholar 

  29. 29

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

    CAS  Article  Google Scholar 

  30. 30

    Chang, C. R. et al. A lethal de novo mutation in the middle domain of the dynamin-related GTPase Drp1 impairs higher order assembly and mitochondrial division. J. Biol. Chem. 285, 32494–32503 (2010)

    CAS  Article  Google Scholar 

  31. 31

    Graham, M. E. et al. The in vivo phosphorylation sites of rat brain dynamin I. J. Biol. Chem. 282, 14695–14707 (2007)

    CAS  Article  Google Scholar 

  32. 32

    Rush, J. et al. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nature Biotechnol. 23, 94–101 (2004)

    Article  Google Scholar 

  33. 33

    Low, H. H. & Lowe, J. Dynamin architecture–from monomer to polymer. Curr. Opin. Struct. Biol. 20, 791–798 (2010)

    CAS  Article  Google Scholar 

  34. 34

    Wang, L. et al. Dynamin 2 mutants linked to centronuclear myopathies form abnormally stable polymers. J. Biol. Chem. 285, 22753–22757 (2010)

    CAS  Article  Google Scholar 

  35. 35

    Low, H. H. et al. 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 

  36. 36

    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 10.1073/pnas.1012792108. (10 January 2011)

  37. 37

    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)

    ADS  CAS  Article  Google Scholar 

  38. 38

    Klockow, B. et al. The dynamin A ring complex: molecular organization and nucleotide-dependent conformational changes. EMBO J. 21, 240–250 (2002)

    CAS  Article  Google Scholar 

  39. 39

    Morlot, S. et al. Deformation of dynamin helices damped by membrane friction. Biophys. J. 99, 3580–3588 (2010)

    ADS  CAS  Article  Google Scholar 

  40. 40

    Van Duyne, G. D. et al. Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J. Mol. Biol. 229, 105–124 (1993)

    CAS  Article  Google Scholar 

  41. 41

    Kabsch, W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Cryst. 26, 795–800 (1993)

    CAS  Article  Google Scholar 

  42. 42

    McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Cryst. 40, 658–674 (2007)

    CAS  Article  Google Scholar 

  43. 43

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

    Article  Google Scholar 

  44. 44

    Schröder, G. F., Levitt, M. & Brunger, A. T. Super-resolution biomolecular crystallography with low-resolution data. Nature 464, 1218–1222 (2010)

    ADS  Article  Google Scholar 

  45. 45

    Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240–255 (1997)

    CAS  Article  Google Scholar 

  46. 46

    Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)

  47. 47

    Laskowski, R. A. et al. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283–291 (1993)

    CAS  Article  Google Scholar 

  48. 48

    DeLano, W. L. The PyMol Molecular Graphics System version 1.4.1 (Schrödinger, 2011)

    Google Scholar 

  49. 49

    Thompson, J. D., Higgins, D. G. & Gibson, T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680 (1994)

    CAS  Article  Google Scholar 

  50. 50

    Fiser, A., Do, R. K. & Sali, A. Modeling of loops in protein structures. Protein Sci. 9, 1753–1773 (2000)

    CAS  Article  Google Scholar 

  51. 51

    Van Der Spoel, D. et al. GROMACS: fast, flexible, and free. J. Comput. Chem. 26, 1701–1718 (2005)

    CAS  Article  Google Scholar 

  52. 52

    Wang, J. M., Cieplak, P. & Kollman, P. A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 21, 1049–1074 (2000)

    CAS  Article  Google Scholar 

  53. 53

    Jorgensen, W. et al. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926–935 (1983)

    ADS  CAS  Article  Google Scholar 

  54. 54

    Essmann, U. et al. A smooth particle mesh Ewald method. J. Chem. Phys. 103, 8577–8593 (1995)

    ADS  CAS  Article  Google Scholar 

  55. 55

    Darden, T., York, D. & Pedersen, L. Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089–10092 (1993)

    CAS  Article  Google Scholar 

  56. 56

    Hess, B. et al. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 18, 1463–1472 (1997)

    CAS  Article  Google Scholar 

  57. 57

    Prinz, J. H. et al. Markov models of molecular kinetics: generation and validation. J. Chem. Phys. 134, 174105 (2011)

    ADS  Article  Google Scholar 

Download references

Acknowledgements

This project was supported by a grant from the Deutsche Forschungsgemeinschaft (SFB 740/C7 and SFB958/A12 to O.D., SFB740/D7 and SFB958/A04 to F.N., SFB740/C8 and SFB 958/A7 to V.H.), by a Career Development Fellowship of The International Human Frontier Science Program Organization and by the EMBO Young Investigator Program to O.D. We would like to thank S. Werner, M. Papst and S. Kraft for technical assistance, the BESSY staff at BL14.1 for help during data collection, G. Schröder for advice in DEN refinement and U. Heinemann for discussions.

Author information

Affiliations

Authors

Contributions

K.F., Y.P., D.S. and Y.R. performed experiments, K.F., Y.P., S.G., M.H., V.H., F.N. and O.D. designed research, M.H. and. F.N. conducted and analysed molecular modelling and molecular dynamics simulations. K.F. and O.D. wrote the manuscript.

Corresponding authors

Correspondence to Katja Faelber or Oliver Daumke.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

The file contains Supplementary Figures 1-12 with legends and Supplementary Table 1. (PDF 9627 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Faelber, K., Posor, Y., Gao, S. et al. Crystal structure of nucleotide-free dynamin. Nature 477, 556–560 (2011). https://doi.org/10.1038/nature10369

Download citation

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

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