Letter | Published:

Structure of the ESCRT-II endosomal trafficking complex

Nature volume 431, pages 221225 (09 September 2004) | Download Citation



The multivesicular-body (MVB) pathway delivers transmembrane proteins and lipids to the lumen of the endosome. The multivesicular-body sorting pathway has crucial roles in growth-factor-receptor downregulation1, developmental signalling2,3,4, regulation of the immune response5 and the budding of certain enveloped viruses such as human immunodeficiency virus6. Ubiquitination is a signal for sorting into the MVB pathway7,8, which also requires the functions of three protein complexes, termed ESCRT-I, -II and -III (endosomal sorting complex required for transport)7,9,10. Here we report the crystal structure of the core of the yeast ESCRT-II complex, which contains one molecule of the Vps protein Vps22, the carboxy-terminal domain of Vps36 and two molecules of Vps25, and has the shape of a capital letter ‘Y’. The amino-terminal coiled coil of Vps22 and the flexible linker leading to the ubiquitin-binding NZF domain of Vps36 both protrude from the tip of one branch of the ‘Y’. Vps22 and Vps36 form nearly equivalent interactions with the two Vps25 molecules at the centre of the ‘Y’. The structure suggests how ubiquitinated cargo could be passed between ESCRT components of the MVB pathway through the sequential transfer of ubiquitinated cargo from one complex to the next.

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  1. 1.

    , , & Multivesicular endosomes containing internalized EGF-EGF receptor complexes mature and then fuse directly with lysosomes. J. Cell Biol. 132, 1011–1023 (1996)

  2. 2.

    , & Xenopus neuralized is a ubiquitin ligase that interacts with XDelta1 and regulates Notch signaling. Dev. Cell 1, 795–806 (2001)

  3. 3.

    , , & Drosophila neuralized is a ubiquitin ligase that promotes the internalization and degradation of Delta. Dev. Cell 1, 783–794 (2001)

  4. 4.

    et al. neuralized encodes a peripheral membrane protein involved in Delta signaling and endocytosis. Dev. Cell 1, 807–816 (2001)

  5. 5.

    et al. Reorganization of multivesicular bodies regulates MHC class II antigen presentation by dendritic cells. J. Cell Biol. 155, 53–63 (2001)

  6. 6.

    et al. Tsg101 and the vacuolar protein sorting pathway are essential for HIV-1 budding. Cell 107, 55–65 (2001)

  7. 7.

    , & Ubiquitin-dependent sorting into the multivesicular body pathway requires the function of a conserved endosomal protein sorting complex, ESCRT-I. Cell 106, 145–155 (2001)

  8. 8.

    & Sorting of proteins into multivesicular bodies: ubiquitin-dependent and -independent targeting. EMBO J. 20, 5176–5186 (2001)

  9. 9.

    , , , & Endosome-associated complex, ESCRT-II, recruits transport machinery for protein sorting at the multivesicular body. Dev. Cell 3, 283–289 (2002)

  10. 10.

    , , , & ESCRT-III: An endosome-associated heterooligomeric protein complex required for MVB sorting. Dev. Cell 3, 271–282 (2002)

  11. 11.

    , , , & Biogenesis of the vacuole in Saccharomyces cerevisiae. Int. Rev.Cytol. 139, 59–120 (1992)

  12. 12.

    , & Receptor downregulation and multivesicular-body sorting. Nature Rev. Mol. Cell Biol. 3, 893–905 (2002)

  13. 13.

    , , & Vps27 recruits ESCRT machinery to endosomes during MVB sorting. J. Cell Biol. 162, 413–423 (2003)

  14. 14.

    , , & Hrs regulates multivesicular body formation via ESCRT recruitment to endosomes. J. Cell Biol. 162, 435–442 (2003)

  15. 15.

    , , & The Vps27p-Hse1p complex binds ubiquitin and mediates endosomal protein sorting. Nature Cell Biol. 4, 534–539 (2002)

  16. 16.

    , , , & TSG101 interaction with HRS mediates endosomal trafficking and receptor down-regulation. Proc. Natl Acad. Sci. USA 100, 7626–7631 (2003)

  17. 17.

    , , & The Vps4p AAA ATPase regulates membrane association of a Vps protein complex required for normal endosome function. EMBO J. 17, 2982–2993 (1998)

  18. 18.

    & Winged helix proteins. Curr. Opin. Struct. Biol. 10, 110–116 (2000)

  19. 19.

    et al. Ubiquitin interactions of NZF zinc fingers. EMBO J. 23, 1411–1421 (2004)

  20. 20.

    et al. Structure and ubiquitin binding of the ubiquitin-interacting motif. J. Biol. Chem. 278, 28976–28984 (2003)

  21. 21.

    , , , & Solution structure of Vps27 UIM-ubiquitin complex important for endosomal sorting and receptor downregulation. EMBO J. 22, 4597–4606 (2003)

  22. 22.

    et al. Ubiquitin recognition by the human TSG101 protein. Mol. Cell 13, 783–789 (2004)

  23. 23.

    , & Structural insights into ESCRT-I recognition of ubiquitinated proteins. J. Biol. Chem.in the press

  24. 24.

    A modular polycistronic expression system for overexpressing protein complexes in Escherichia coli. Protein Expr. Purif. 21, 224–234 (2001)

  25. 25.

    & Automated MAD and MIR structure solution. Acta Crystallogr. D Biol. Crystallogr. 55, 849–861 (1999)

  26. 26.

    Maximum-likelihood density modification. Acta Crystallogr. D Biol. Crystallogr. 56, 965–972 (2000)

  27. 27.

    , , & 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)

  28. 28.

    & The PredictProtein server. Nucleic Acids Res. 31, 3300–3304 (2003)

  29. 29.

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

  30. 30.

    , & Fab1p PtdIns(3)P 5-kinase function essential for protein sorting in the multivesicular body. Cell 95, 847–858 (1998)

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We thank P. P. di Fiore, M. Babst and B. Wendland for helpful discussions; M. Tabuchi for the Flag tag construct; and we acknowledge the use of the SER-CAT beamline at the APS, ANL and beamline 9-2 at the Stanford Synchrotron Radiation Laboratory. Use of the Advanced Photon Source was supported by the US Department of Energy, Basic Energy Sciences, Office of Science. The Stanford Synchrotron Radiation Laboratory, a national user facility operated by Stanford University on behalf of the US Department of Energy, is supported by the Department of Energy, Office of Biological and Environmental Research, and by the National Institutes of Health, National Center for Research Resources, Biomedical Technology Program and the National Institute of General Medical Sciences. S.D.E. is supported as an Investigator of the Howard Hughes Medical Institute.

Author information


  1. Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland 20892-0580, USA

    • Aitor Hierro
    • , Jaewon Kim
    • , Gali Prag
    •  & James H. Hurley
  2. Department of Cellular and Molecular Medicine and Department of Chemistry and Biochemistry and Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0668, USA

    • Ji Sun
    • , Alexander S. Rusnak
    •  & Scott D. Emr


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Competing interests

The authors declare that they have no competing financial interests.

Corresponding author

Correspondence to James H. Hurley.

Supplementary information

Image files

  1. 1.

    Supplementary Figure 1

    Structures of ESCRT-II subunits. a. Structure of Vps22. b. Structure of Vps25. c. Structure of Vps36.

  2. 2.

    Supplementary Figure 2

    Sequence conservation in ESCRT-II. a, Structure-based alignment of Vps22 and homologues with amino acids highlighted in red (identical in all species), and orange (conserved in at least four of five species shown). b, Vps25 and homologues; c, Vps36 C-terminal domain and homologues.

  3. 3.

    Supplementary Figure 3

    Trafficking of ubiquitinated membrane proteins by ESCRTs. ESCRT-I binds Ub-cargo through the UEV domain of Vps23 23. The second NZF domain of Vps36 binds Ub-cargo

PDF files

  1. 1.

    Supplementary Table 1

    Crystallographic data Collection, Phasing, and Refinement Statistics.

  2. 2.

    Supplementary Table 2

    Mutational analysis of ESCRT-II assembly and function.

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