Structure of the Sec23/24–Sar1 pre-budding complex of the COPII vesicle coat

Article metrics

Abstract

COPII-coated vesicles form on the endoplasmic reticulum by the stepwise recruitment of three cytosolic components: Sar1–GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerization and membrane deformation. Crystallographic analysis of the Saccharomyces cerevisiae Sec23/24–Sar1 complex reveals a bow-tie-shaped structure, 15 nm long, with a membrane-proximal surface that is concave and positively charged to conform to the size and acidic-phospholipid composition of the COPII vesicle. Sec23 and Sar1 form a continuous surface stabilized by a non-hydrolysable GTP analogue, and Sar1 has rearranged from the GDP conformation to expose amino-terminal residues that will probably embed in the bilayer. The GTPase-activating protein (GAP) activity of Sec23 involves an arginine side chain inserted into the Sar1 active site. These observations establish the structural basis for GTP-dependent recruitment of a vesicular coat complex, and for uncoating through coat-controlled GTP hydrolysis.

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 the Sec23/24–Sar1 pre-budding complex.
Figure 2: Domain structure and relatedness of Sec23 and Sec24.
Figure 3: Surface features of the Sec23/24 complex a, Molecular surface coloured according to electrostatic potential50: negative potential is red and positive potential blue.
Figure 4: Conformational switching and protein–protein interactions.
Figure 5: GTP-dependent coat recruitment and coat-dependent GTP hydrolysis a, Stereo view showing interactions between Sar1–GppNHp (pink) and Sec23 (coloured as in Fig. 2).

References

  1. 1

    Mellman, I. & Warren, G. The road taken: past and future foundations of membrane traffic. Cell 100, 99–112 (2000)

  2. 2

    Kirchhausen, T. Three ways to make a vesicle. Nature Rev. Mol. Cell Biol. 1, 187–198 (2000)

  3. 3

    Serafini, T. et al. ADP-ribosylation factor is a subunit of the coat of Golgi-derived COP-coated vesicles: a novel role for a GTP-binding protein. Cell 67, 239–253 (1991)

  4. 4

    Donaldson, J. G., Cassel, D., Kahn, R. A. & Klausner, R. D. ADP-ribosylation factor, a small GTP-binding protein, is required for binding of the coatomer protein β-COP to Golgi membranes. Proc. Natl Acad. Sci. USA 89, 6408–6412 (1992)

  5. 5

    Barlowe, C. et al. COPII: a membrane coat formed by Sec proteins that drive vesicle budding from the endoplasmic reticulum. Cell 77, 895–907 (1994)

  6. 6

    Tanigawa, G. et al. Hydrolysis of bound GTP by ARF protein triggers uncoating of Golgi-derived COP-coated vesicles. J. Cell Biol. 123, 1365–1371 (1993)

  7. 7

    Yoshihisa, T., Barlowe, C. & Schekman, R. Requirement for a GTPase-activating protein in vesicle budding from the endoplasmic reticulum. Science 259, 1466–1468 (1993)

  8. 8

    Antonny, B., Madden, D., Hamamoto, S., Orci, L. & Schekman, R. Dynamics of the COPII coat with GTP and stable analogues. Nature Cell Biol. 3, 531–537 (2001)

  9. 9

    Nagahama, M. et al. A v-SNARE implicated in intra-Golgi transport. J. Cell Biol. 133, 507–516 (1996)

  10. 10

    Springer, S. & Schekman, R. Nucleation of COPII vesicular coat complex by endoplasmic reticulum to Golgi vesicle SNAREs. Science 281, 698–700 (1998)

  11. 11

    Grabowski, R. & Gallwitz, D. High-affinity binding of the yeast cis-Golgi t-SNARE, Sed5p, to wild-type and mutant Sly1p, a modulator of transport vesicle docking. FEBS Lett. 411, 169–172 (1997)

  12. 12

    Matsuoka, K. et al. COPII-coated vesicle formation reconstituted with purified coat proteins and chemically defined liposomes. Cell 93, 263–275 (1998)

  13. 13

    Nakano, A., Brada, D. & Schekman, R. A membrane glycoprotein, Sec12p, required for protein transport from the endoplasmic reticulum to the Golgi apparatus in yeast. J. Cell Biol. 107, 851–863 (1988)

  14. 14

    Barlowe, C. & Schekman, R. SEC12 encodes a guanine-nucleotide-exchange factor essential for transport vesicle budding from the ER. Nature 365, 347–349 (1993)

  15. 15

    Weissman, J. T., Plutner, H. & Balch, W. E. The mammalian guanine nucleotide exchange factor mSec12 is essential for activation of the Sar1 GTPase directing endoplasmic reticulum export. Traffic 2, 465–475 (2001)

  16. 16

    Huang, M. et al. Crystal structure of Sar1-GDP at 1.7 Å resolution and the role of the NH2 terminus in ER export. J. Cell Biol. 155, 937–948 (2001)

  17. 17

    Amor, J. C., Harrison, D. H., Kahn, R. A. & Ringe, D. Structure of the human ADP-ribosylation factor 1 complexed with GDP. Nature 372, 704–708 (1994)

  18. 18

    Antonny, B., Beraud-Dufour, S., Chardin, P. & Chabre, M. N-terminal hydrophobic residues of the G-protein ADP-ribosylation factor-1 insert into membrane phospholipids upon GDP to GTP exchange. Biochemistry 36, 4675–4684 (1997)

  19. 19

    Goldberg, J. Structural basis for activation of ARF GTPase: mechanisms of guanine nucleotide exchange and GTP-myristoyl switching. Cell 95, 237–248 (1998)

  20. 20

    Beraud-Dufour, S., Paris, S., Chabre, M. & Antonny, B. Dual interaction of ADP ribosylation factor 1 with Sec7 domain and with lipid membranes during catalysis of guanine nucleotide exchange. J. Biol Chem. 274, 37629–37636 (1999)

  21. 21

    Lederkremer, G. Z. et al. Structure of the Sec23p/24p and Sec13p/31p complexes of COPII. Proc. Natl Acad. Sci. USA 98, 10704–10709 (2001)

  22. 22

    Matsuoka, K., Schekman, R., Orci, L. & Heuser, J. E. Surface structure of the COPII-coated vesicle. Proc. Natl Acad. Sci. USA 98, 13705–13709 (2001)

  23. 23

    Kuehn, M. J., Herrmann, J. M. & Schekman, R. COPII-cargo interactions direct protein sorting into ER-derived transport vesicles. Nature 391, 187–190 (1998)

  24. 24

    Aridor, M., Weissman, J., Bannykh, S., Nuoffer, C. & Balch, W. E. Cargo selection by the COPII budding machinery during export from the ER. J. Cell Biol. 141, 61–70 (1998)

  25. 25

    Peng, R., Grabowski, R., De Antoni, A. & Gallwitz, D. Specific interaction of the yeast cis-Golgi syntaxin Sed5p and the coat protein complex II component Sec24p of endoplasmic reticulum-derived transport vesicles. Proc. Natl Acad. Sci. USA 96, 3751–3756 (1999)

  26. 26

    Votsmeier, C. & Gallwitz, D. An acidic sequence of a putative yeast Golgi membrane protein binds COPII and facilitates ER export. EMBO J. 20, 6742–6750 (2001)

  27. 27

    Martinez-Menarguez, J. A., Geuze, H. J., Slot, J. W. & Klumperman, J. Vesicular tubular clusters between the ER and Golgi mediate concentration of soluble secretory proteins by exclusion from COPI-coated vesicles. Cell 98, 81–90 (1999)

  28. 28

    Balch, W. E., McCaffery, J. M., Plutner, H. & Farquhar, M. G. Vesicular stomatitis virus glycoprotein is sorted and concentrated during export from the endoplasmic reticulum. Cell 76, 841–852 (1994)

  29. 29

    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)

  30. 30

    Collins, B. M., McCoy, A. J., Kent, H. M., Evans, P. R. & Owen, D. J. Molecular architecture and functional model of the endocytic AP2 complex. Cell 109, 523–535 (2002)

  31. 31

    Huang, M., Weissman, J. T., Wang, C., Balch, W. E. & Wilson, I. A. Protein engineering for crystallization of the GTPase Sar1 that regulates ER vesicle budding. Acta Crystallogr. D 58, 700–703 (2002)

  32. 32

    Paris, S. et al. Role of protein–phospholipid interactions in the activation of ARF1 by the guanine nucleotide exchange factor Arno. J. Biol. Chem. 272, 22221–22226 (1997)

  33. 33

    Goldberg, J. Structural and functional analysis of the ARF1–ARFGAP complex reveals a role for coatomer in GTP hydrolysis. Cell 96, 893–902 (1999)

  34. 34

    Pasqualato, S., Menetrey, J., Franco, M. & Cherfils, J. The structural GDP/GTP cycle of human Arf6. EMBO Rep. 2, 234–238 (2001)

  35. 35

    Hanzal-Bayer, M., Renault, L., Roversi, P., Wittinghofer, A. & Hillig, R. C. The complex of Arl2-GTP and PDEδ: from structure to function. EMBO J. 21, 2095–2106 (2002)

  36. 36

    Shimoni, Y. et al. Lst1p and Sec24p cooperate in sorting of the plasma membrane ATPase into COPII vesicles in Saccharomyces cerevisiae. J. Cell Biol. 151, 973–984 (2000)

  37. 37

    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)

  38. 38

    Ponting, C. P., Aravind, L., Schultz, J., Bork, P. & Koonin, E. V. Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer. J. Mol. Biol. 289, 729–745 (1999)

  39. 39

    Robinson, R. C. et al. Domain movement in gelsolin: a calcium-activated switch. Science 286, 1939–1942 (1999)

  40. 40

    Peng, R., De Antoni, A. & Gallwitz, D. Evidence for overlapping and distinct functions in protein transport of coat protein Sec24p family members. J. Biol. Chem. 275, 11521–11528 (2000)

  41. 41

    Franco, M., Chardin, P., Chabre, M. & Paris, S. Myristoylation is not required for GTP-dependent binding of ADP-ribosylation factor ARF1 to phospholipids. J. Biol. Chem. 268, 24531–24534 (1993)

  42. 42

    Franco, M., Chardin, P., Chabre, M. & Paris, S. Myristoylation-facilitated binding of the G protein ARF1GDP to membrane phospholipids is required for its activation by a soluble nucleotide exchange factor. J. Biol. Chem. 271, 1573–1578 (1996)

  43. 43

    Randazzo, P. A. Functional interaction of ADP-ribosylation factor 1 with phosphatidylinositol 4,5-bisphosphate. J. Biol. Chem. 272, 7688–7692 (1997)

  44. 44

    Scheffzek, K., Ahmadian, M. R. & Wittinghofer, A. GTPase-activating proteins: helping hands to complement an active site. Trends Biochem. Sci. 23, 257–262 (1998)

  45. 45

    Shaywitz, D. A., Espenshade, P. J., Gimeno, R. E. & Kaiser, C. A. COPII subunit interactions in the assembly of the vesicle coat. J. Biol. Chem. 272, 25413–25416 (1997)

  46. 46

    Otwinoski, W. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)

  47. 47

    Terwilliger, T. C. & Berendzen, J. Automated MAD and MIR structure solution. Acta Crystallogr. D 55, 849–861 (1999)

  48. 48

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

  49. 49

    Brunger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)

  50. 50

    Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281–296 (1991)

Download references

Acknowledgements

We thank E. Mossessova for the Sar1 expression construct, J. Walker for assistance and advice on data collection and processing, C. Heaton for use of synchrotron facilities at CHESS, and M. Becker at NSLS. This work was supported by grants from the National Institutes of Health, the Howard Hughes Medial Institute, and the Pew Scholars Program in the Biomedical Sciences.

Author information

Correspondence to Jonathan Goldberg.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Bi, X., Corpina, R. & Goldberg, J. Structure of the Sec23/24–Sar1 pre-budding complex of the COPII vesicle coat. Nature 419, 271–277 (2002) doi:10.1038/nature01040

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.