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Molecular model for a complete clathrin lattice from electron cryomicroscopy

Abstract

Clathrin-coated vesicles are important vehicles of membrane traffic in cells. We report the structure of a clathrin lattice at subnanometre resolution, obtained from electron cryomicroscopy of coats assembled in vitro. We trace most of the 1,675-residue clathrin heavy chain by fitting known crystal structures of two segments, and homology models of the rest, into the electron microscopy density map. We also define the position of the central helical segment of the light chain. A helical tripod, the carboxy-terminal parts of three heavy chains, projects inward from the vertex of each three-legged clathrin triskelion, linking that vertex to ‘ankles’ of triskelions centred two vertices away. Analysis of coats with distinct diameters shows an invariant pattern of contacts in the neighbourhood of each vertex, with more variable interactions along the extended parts of the triskelion ‘legs’. These invariant local interactions appear to stabilize the lattice, allowing assembly and uncoating to be controlled by events at a few specific sites.

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Figure 1: The clathrin triskelion and the designs of some simple clathrin lattices.
Figure 2: Image reconstruction of a clathrin hexagonal barrel (heavy chains only) at 7.9 Å resolution.
Figure 3: Rigid-body fit of the atomic model for a segment of the proximal leg17 to the density from the cryoEM image reconstruction.
Figure 4: Backbone model for residues 1–1597 of the clathrin heavy chain.
Figure 5: The hub assembly.
Figure 6: Model for clathrin light chains.
Figure 7: How clathrin forms lattices with different curvature: the mini-coat.

References

  1. Kirchhausen, T. Clathrin. Annu. Rev. Biochem. 69, 699–727 (2000)

    CAS  Article  Google Scholar 

  2. Robinson, M. S. Adaptable adaptors for coated vesicles. Trends Cell Biol. 14, 167–174 (2004)

    CAS  Article  Google Scholar 

  3. Brodsky, F. M., Chen, C. Y., Knuehl, C., Towler, M. C. & Wakeham, D. E. Biological basket weaving: formation and function of clathrin-coated vesicles. Annu. Rev. Cell Dev. Biol. 17, 517–568 (2001)

    CAS  Article  Google Scholar 

  4. Crowther, R. A., Finch, J. T. & Pearse, B. M. On the structure of coated vesicles. J. Mol. Biol. 103, 785–798 (1976)

    CAS  Article  Google Scholar 

  5. Kirchhausen, T. & Harrison, S. C. Protein organization in clathrin trimers. Cell 23, 755–761 (1981)

    CAS  Article  Google Scholar 

  6. Ungewickell, E. & Branton, D. Assembly units of clathrin coats. Nature 289, 420–422 (1981)

    ADS  CAS  Article  Google Scholar 

  7. Kirchhausen, T., Harrison, S. C. & Heuser, J. Configuration of clathrin trimers: Evidence from electron microscopy. J. Ultrastruct. Mol. Struct. Res. 94, 199–208 (1986)

    CAS  Article  Google Scholar 

  8. Ungewickell, E. Biochemical and immunological studies on clathrin light chains and their binding sites on clathrin triskelions. EMBO J. 8, 1401–1408 (1983)

    Article  Google Scholar 

  9. Kirchhausen, T., Harrison, S. C., Parham, P. & Brodsky, F. M. Location and distribution of the light chains in clathrin trimers. Proc. Natl Acad. Sci. USA 80, 2481–2485 (1983)

    ADS  CAS  Article  Google Scholar 

  10. Kirchhausen, T. et al. Clathrin light chains LCA and LCB are similar, polymorphic and share repeated heptad motifs. Science 236, 320–324 (1987)

    ADS  CAS  Article  Google Scholar 

  11. Jackson, A. P., Seow, H. F., Holmes, N., Drickamer, K. & Parham, P. Clathrin light chains contain brain-specific insertion sequences and a region of homology with intermediate filaments. Nature 326, 154–159 (1987)

    ADS  CAS  Article  Google Scholar 

  12. Vigers, G. P., Crowther, R. A. & Pearse, B. M. Three-dimensional structure of clathrin cages in ice. EMBO J. 5, 529–534 (1986)

    CAS  Article  Google Scholar 

  13. Vigers, G. P., Crowther, R. A. & Pearse, B. M. Location of the 100 kd-50 kd accessory proteins in clathrin coats. EMBO J. 5, 2079–2085 (1986)

    CAS  Article  Google Scholar 

  14. Smith, C. J., Grigorieff, N. & Pearse, B. M. Clathrin coats at 21 Å resolution: a cellular assembly designed to recycle multiple membrane receptors. EMBO J. 17, 4943–4953 (1998)

    CAS  Article  Google Scholar 

  15. Musacchio, A. et al. Functional organization of clathrin in coats: combining electron cryomicroscopy and X-ray crystallography. Mol. Cell 3, 761–770 (1999)

    CAS  Article  Google Scholar 

  16. Ter Haar, E., Musacchio, A., Harrison, S. C. & Kirchhausen, T. Atomic structure of clathrin—a β propeller terminal domain joins an α zigzag linker. Cell 95, 563–573 (1998)

    CAS  Article  Google Scholar 

  17. Ybe, J. A. et al. Clathrin self-assembly is mediated by a tandemly repeated superhelix. Nature 399, 371–375 (1999)

    ADS  CAS  Article  Google Scholar 

  18. Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003)

    CAS  Article  Google Scholar 

  19. Liu, S.-H., Wong, M. L., Craik, C. S. & Brodsky, F. M. Regulation of clathrin assembly and trimerization defined using recombinant triskelion hubs. Cell 83, 257–267 (1995)

    CAS  Article  Google Scholar 

  20. Kirchhausen, T. & Toyoda, T. Immunoelectron microscopic evidence for the extended conformation of light chains in clathrin trimers. J. Biol. Chem. 268, 10268–10273 (1993)

    CAS  PubMed  Google Scholar 

  21. Scarmato, P. & Kirchhausen, T. Analysis of clathrin light chain-heavy chain interactions using truncated mutants of rat liver light chain LCB3. J. Biol. Chem. 265, 3661–3668 (1990)

    CAS  PubMed  Google Scholar 

  22. Nathke, I. S. et al. Folding and trimerization of clathrin subunits at the triskelion hub. Cell 68, 899–910 (1992)

    CAS  Article  Google Scholar 

  23. Chen, C. Y. et al. Clathrin light and heavy chain interface: alpha-helix binding superhelix loops via critical tryptophans. EMBO J. 21, 6072–6082 (2002)

    CAS  Article  Google Scholar 

  24. Ungewickell, E. et al. Role of auxilin in uncoating clathrin-coated vesicles. Nature 378, 632–635 (1995)

    ADS  CAS  Article  Google Scholar 

  25. Heuser, J. Three-dimensional visualization of coated vesicle formation in fibroblasts. J. Cell Biol. 84, 560–583 (1980)

    CAS  Article  Google Scholar 

  26. Ehrlich, M. et al. Endocytosis by random initiation and stabilization of clathrin-coated pits. Cell 118, 591–605 (2004)

    CAS  Article  Google Scholar 

  27. Fotin, A. et al. Structure of an auxilin-bound clathrin coat and its implications for the mechanism of uncoating. Nature doi:10.1038/nature03078 (this issue)

  28. Matsui, W. & Kirchhausen, T. Stabilization of clathrin coats by the core of the clathrin-associated protein complex AP-2. Biochemistry 29, 10791–10798 (1990)

    CAS  Article  Google Scholar 

  29. Thon, F. Zur Defokussierungsabhängigkeit des Phasenkontrastes bei der elektronenmikroskopischen Abbildung. Z. Naturforsch. 21a, 476–478 (1966)

    ADS  Google Scholar 

  30. van Heel, M., Harauz, G., Orlova, E. V., Schmidt, R. & Schatz, M. A new generation of the IMAGIC image processing system. J. Struct. Biol. 116, 17–24 (1996)

    CAS  Article  Google Scholar 

  31. van Heel, M. et al. Single-particle electron cryo-microscopy: towards atomic resolution. Q. Rev. Biophys. 33, 307–369 (2000)

    CAS  Article  Google Scholar 

  32. Mindell, J. A. & Grigorieff, N. Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142, 334–347 (2003)

    Article  Google Scholar 

  33. Grigorieff, N. Three-dimensional structure of bovine NADH:ubiquinone oxidoreductase (complex I) at 22 Å in ice. J. Mol. Biol. 277, 1033–1046 (1998)

    CAS  Article  Google Scholar 

  34. Ludtke, S. J., Baldwin, P. R. & Chiu, W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128, 82–97 (1999)

    CAS  Article  Google Scholar 

  35. Huang, C. C., Couch, G. S., Pettersen, E. F. & Ferrin, T. E. Chimera: an extensible molecular modeling application constructed using standard components. Pacif. Symp. Biocomput. 1, 724 (1996)

    Google Scholar 

  36. Jones, T. A., Zou, J.-Y. & Cowan, S. W. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991)

    Article  Google Scholar 

  37. Jones, T. A. (ed.) A, yaap, asap, @#*? A Set of Averaging Programs (SERC Daresbury Laboratory, Warrington, 1992)

  38. Kleywegt, G. J. & Jones, T. A. Software for handling macromolecular envelopes. Acta Crystallogr. D 55, 941–944 (1999)

    CAS  Article  Google Scholar 

  39. Marti-Renom, M. A. et al. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291–325 (2000)

    CAS  Article  Google Scholar 

  40. Sali, A. & Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779–815 (1993)

    CAS  Article  Google Scholar 

  41. Collaborative Computational Project. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D50, 760–763 (1994)

    Google Scholar 

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Acknowledgements

Authors N.G., S.C.H., T.K. and T.W. are listed alphabetically. We thank W. Boll and I. Rapoport for help in the purification of clathrin and adaptors. This work was supported by NIH grants to T.K. and to D. De Rosier (Brandeis University). N.G. and S.C.H. are investigators in the Howard Hughes Medical Institute.

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Correspondence to Stephen C. Harrison.

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Fotin, A., Cheng, Y., Sliz, P. et al. Molecular model for a complete clathrin lattice from electron cryomicroscopy. Nature 432, 573–579 (2004). https://doi.org/10.1038/nature03079

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