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Glycoprotein organization of Chikungunya virus particles revealed by X-ray crystallography

Nature volume 468, pages 709–712 (2010)Cite this article

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Abstract

Chikungunya virus (CHIKV) is an emerging mosquito-borne alphavirus that has caused widespread outbreaks of debilitating human disease in the past five years1. CHIKV invasion of susceptible cells is mediated by two viral glycoproteins, E1 and E2, which carry the main antigenic determinants and form an icosahedral shell at the virion surface. Glycoprotein E2, derived from furin cleavage of the p62 precursor into E3 and E2, is responsible for receptor binding, and E1 for membrane fusion. In the context of a concerted multidisciplinary effort to understand the biology of CHIKV2, here we report the crystal structures of the precursor p62–E1 heterodimer and of the mature E3–E2–E1 glycoprotein complexes. The resulting atomic models allow the synthesis of a wealth of genetic, biochemical, immunological and electron microscopy data accumulated over the years on alphaviruses in general. This combination yields a detailed picture of the functional architecture of the 25 MDa alphavirus surface glycoprotein shell. Together with the accompanying report on the structure of the Sindbis virus E2–E1 heterodimer at acidic pH (ref. 3), this work also provides new insight into the acid-triggered conformational change on the virus particle and its inbuilt inhibition mechanism in the immature complex.

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Figure 1: Structure of the p62–E1 heterodimer.
Figure 2: The E1 fusion loop binding groove in E2.
Figure 3: Combination with cryo-EM data.
Figure 4: p62 maturation and low pH conformational transition.

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Accession codes

Primary accessions

Protein Data Bank

Data deposits

Structure factors and coordinates for the structures of the p62–E1 (crystal IO), E3–E2–E1sp (crystal MM), E3–E2–E1f (crystal MO1), E3–E2–E1t (crystal MO2) and Os2-E3–E2–E1t (crystal MO3) complexes have been deposited in the Protein Data Bank under accession codes 3N40, 3N41, 3N42, 3N43 and 3N44, respectively. The coordinates of the molecules fitted in the cryo-EM 3D reconstructions of SINV and SFV particles were deposited under accession codes 2XFB and 2XFC, respectively.

References

  1. Her, Z., Kam, Y. W., Lin, R. T. & Ng, L. F. Chikungunya: a bending reality. Microbes Infect. 11, 1165–1176 (2009)

    Article  PubMed  Google Scholar 

  2. Schwartz, O. & Albert, M. L. Biology and pathogenesis of chikungunya virus. Nature Rev. Microbiol. 8, 491–500 (2010)

    Article  CAS  Google Scholar 

  3. Li, L., Jose, J., Xiang, Y., Kuhn, R. J. & Rossmann, M. G. Structural changes of envelope proteins during alphavirus fusion. Nature 10.1038/nature09546 (this issue)

  4. Halstead, S. B. in Pediatric Infectious Diseases (eds Feigin, R. & Cherry, J.) 2178–2183 (Saunders, 2004)

    Google Scholar 

  5. Robinson, M. C. An epidemic of virus disease in southern province, Tanganyika territory, in 1952–1953 I. Clinical features. Trans. R. Soc. Trop. Med. Hyg. 49, 28–32 (1955)

    Article  CAS  PubMed  Google Scholar 

  6. Johnson, F. Notes on Kimakonde. Bull. Sch. Orient. Studies 2, 417–466 (1922)

    Article  Google Scholar 

  7. Carey, D. E. Chikungunya and dengue: a case of mistaken identity? J. Hist. Med. Allied Sci. 26, 243–262 (1971)

    Article  CAS  PubMed  Google Scholar 

  8. Schuffenecker, I. et al. Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak. PLoS Med. 3, e263 (2006)

    Article  PubMed  PubMed Central  Google Scholar 

  9. Tsetsarkin, K. A., Vanlandingham, D. L., McGee, C. E. & Higgs, S. A single mutation in chikungunya virus affects vector specificity and epidemic potential. PLoS Pathog. 3, e201 (2007)

    Article  PubMed  PubMed Central  Google Scholar 

  10. Vazeille, M. et al. Two chikungunya isolates from the outbreak of La Reunion (Indian Ocean) exhibit different patterns of infection in the mosquito, aedes albopictus . PLoS ONE 2, e1168 (2007)

    Article  ADS  PubMed  PubMed Central  Google Scholar 

  11. Enserink, M. Entomology: a mosquito goes global. Science 320, 864–866 (2008)

    Article  CAS  PubMed  Google Scholar 

  12. Akahata, W. et al. A virus-like particle vaccine for epidemic chikungunya virus protects nonhuman primates against infection. Nature Med. 16, 334–338 (2010)

    Article  CAS  PubMed  Google Scholar 

  13. Salminen, A. et al. Membrane fusion process of Semliki Forest virus. II. Cleavage-dependent reorganization of the spike protein complex controls virus entry. J. Cell Biol. 116, 349–357 (1992)

    Article  CAS  PubMed  Google Scholar 

  14. Ziemiecki, A., Garoff, H. & Simons, K. Formation of the Semliki Forest virus membrane glycoprotein complexes in the infected cell. J. Gen. Virol. 50, 111–123 (1980)

    Article  CAS  PubMed  Google Scholar 

  15. Marsh, M. & Helenius, A. Virus entry into animal cells. Adv. Virus Res. 36, 107–151 (1989)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Wahlberg, J. M., Boere, W. A. & Garoff, H. The heterodimeric association between the membrane proteins of Semliki Forest virus changes its sensitivity to low pH during virus maturation. J. Virol. 63, 4991–4997 (1989)

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Kielian, M. & Helenius, A. pH-induced alterations in the fusogenic spike protein of Semliki Forest virus. J. Cell Biol. 101, 2284–2291 (1985)

    Article  CAS  PubMed  Google Scholar 

  18. Wahlberg, J. M., Bron, R., Wilschut, J. & Garoff, H. Membrane fusion of Semliki Forest virus involves homotrimers of the fusion protein. J. Virol. 66, 7309–7318 (1992)

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Lescar, J. et al. The fusion glycoprotein shell of Semliki Forest virus: an icosahedral assembly primed for fusogenic activation at endosomal pH. Cell 105, 137–148 (2001)

    Article  CAS  PubMed  Google Scholar 

  20. Gibbons, D. L. et al. Conformational change and protein–protein interactions of the fusion protein of Semliki Forest virus. Nature 427, 320–325 (2004)

    Article  ADS  CAS  PubMed  Google Scholar 

  21. Kielian, M. & Rey, F. A. Virus membrane-fusion proteins: more than one way to make a hairpin. Nature Rev. Microbiol. 4, 67–76 (2006)

    Article  CAS  Google Scholar 

  22. Rey, F. A. et al. The envelope glycoprotein from tick-borne encephalitis virus at 2 Å resolution. Nature 375, 291–298 (1995)

    Article  ADS  CAS  PubMed  Google Scholar 

  23. Lobigs, M., Zhao, H. X. & Garoff, H. Function of Semliki Forest virus E3 peptide in virus assembly: replacement of E3 with an artificial signal peptide abolishes spike heterodimerization and surface expression of E1. J. Virol. 64, 4346–4355 (1990)

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Tsetsarkin, K. A. et al. Epistatic roles of E2 glycoprotein mutations in adaption of chikungunya virus to Aedes albopictus and Ae. aegypti mosquitoes. PLoS ONE 4, e6835 (2009)

    Article  ADS  PubMed  PubMed Central  Google Scholar 

  25. Pierro, D. J., Powers, E. L. & Olson, K. E. Genetic determinants of Sindbis virus mosquito infection are associated with a highly conserved alphavirus and flavivirus envelope sequence. J. Virol. 82, 2966–2974 (2008)

    Article  CAS  PubMed  Google Scholar 

  26. Meyer, W. J. & Johnston, R. E. Structural rearrangement of infecting Sindbis virions at the cell surface: mapping of newly accessible epitopes. J. Virol. 67, 5117–5125 (1993)

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Meyer, W. J. et al. Conformational alteration of Sindbis virion glycoproteins induced by heat, reducing agents, or low pH. J. Virol. 66, 3504–3513 (1992)

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Flynn, D. C., Meyer, W. J., Mackenzie, J. M., Jr & Johnston, R. E. A conformational change in Sindbis virus glycoproteins E1 and E2 is detected at the plasma membrane as a consequence of early virus-cell interaction. J. Virol. 64, 3643–3653 (1990)

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Wu, S. R. et al. The dynamic envelope of a fusion class II virus. Prefusion stages of Semliki Forest virus revealed by electron cryomicroscopy. J. Biol. Chem. 282, 6752–6762 (2007)

    Article  CAS  PubMed  Google Scholar 

  30. Mukhopadhyay, S. et al. Mapping the structure and function of the E1 and E2 glycoproteins in alphaviruses. Structure 14, 63–73 (2006)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Schuffenecker, I. et al. Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak. PLoS Med. 3, e263 (2006)

    Article  PubMed  PubMed Central  Google Scholar 

  32. Krey, T. et al. The disulfide bonds in glycoprotein E2 of hepatitis C virus reveal the tertiary organization of the molecule. PLoS Pathog. 6, e1000762 (2010)

    Article  PubMed  PubMed Central  Google Scholar 

  33. Kabsch, W. Integration, scaling, space-group assignment and post-refinement. Acta Crystallogr. D 66, 133–144 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Evans, P. R. Scaling and assessment of data quality. Acta Crystallogr. D 62, 72–82 (2005)

    Article  PubMed  Google Scholar 

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

    Article  Google Scholar 

  36. Navaza, J. Implementation of molecular replacement in AMoRe. Acta Crystallogr. D 57, 1367–1372 (2001)

    Article  CAS  PubMed  Google Scholar 

  37. Roussel, A. et al. Structure and interactions at the viral surface of the envelope protein E1 of Semliki Forest virus. Structure 14, 75–86 (2006)

    Article  CAS  PubMed  Google Scholar 

  38. Bricogne, G. et al. Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0. Acta Crystallogr. D 59, 2023–2030 (2003)

    Article  CAS  PubMed  Google Scholar 

  39. Abrahams, J. P. & Leslie, A. G. Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Crystallogr. D 52, 30–42 (1996)

    Article  CAS  PubMed  Google Scholar 

  40. Cowtan, K. The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr. D 62, 1002–1011 (2006)

    Article  PubMed  Google Scholar 

  41. Cowtan, K. ‘dm’: an automated procedure for phase improvement by density modification. Joint CCP4 ESF-EACBM Newsl. Protein Crystallogr. 31, 34–38 (1994)

    Google Scholar 

  42. Emsley, P. et al. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Bricogne, G. et al. BUSTER version 2.9. (Global Phasing, 2010)

  44. Painter, J. & Merritt, E. A. A molecular viewer for the analysis of TLS rigid-body motion in macromolecules. Acta Crystallogr. D 61, 465–471 (2005)

    Article  PubMed  Google Scholar 

  45. Mukhopadhyay, S. et al. Mapping the structure and function of the E1 and E2 glycoproteins in alphaviruses. Structure 14, 63–73 (2006)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Mancini, E. J. et al. Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus. Mol. Cell 5, 255–266 (2000)

    Article  CAS  PubMed  Google Scholar 

  47. Akahata, W. et al. A virus-like particle vaccine for epidemic Chikungunya virus protects nonhuman primates against infection. Nature Med. 16, 334–338 (2010)

    Article  CAS  PubMed  Google Scholar 

  48. Navaza, J. et al. On the fitting of model electron densities into EM reconstructions: a reciprocal-space formulation. Acta Crystallogr. D 58, 1820–1825 (2002)

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank the CHIKV task force at Institut Pasteur, in particular the group of F. Tangy and the staff of platform PF8 for the CHIKV complementary DNA; A. Haouz of PF6 for crystallogenesis; the staff of synchrotron beamlines PROXIMA 1 at Soleil, ID23-eh2 at the European Synchrotron Radiation Facility and PX-I at the Swiss Light Source; M. Rossmann and Y. Sun for providing the 16 Å cryo-EM map of CHIKV virion-like particles and for sharing the coordinates and manuscript of the low pH structure of the SINV E1–E2 heterodimer before publication; and members of the F.A.R. laboratory for help during data collection. J.E.V. was supported by a Marie Curie fellowship through the European Union Research Traning Network program “Intrapath”. This work was funded in part by the French ‘Agence Nationale de la Recherche’ grant DENtry in the program ‘Microbiologie, Infections et Immunité’, by Merck-Serono, by the Pediatric Dengue Vaccine Initiative and by the Institut Pasteur program PTR201 CHIKV to F.A.R..

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Authors and Affiliations

  1. Département de Virologie, Institut Pasteur, Unité de Virologie Structurale, 25 rue du Dr Roux, 75724 Paris Cedex 15, France,

    James E. Voss, Marie-Christine Vaney, Stéphane Duquerroy & Félix A. Rey

  2. CNRS URA 3015, 25 rue du Dr Roux, 75724 Paris Cedex 15, France ,

    James E. Voss, Marie-Christine Vaney, Stéphane Duquerroy & Félix A. Rey

  3. Université Paris-Sud, Faculté d’Orsay, Orsay Cedex, 91405, France

    Stéphane Duquerroy

  4. Global Phasing Ltd, Sheraton House, Castle Park, Cambridge, CB3 0AX, United Kingdom

    Clemens Vonrhein & Gérard Bricogne

  5. Département de Biologie Structurale et Chimie, Institut Pasteur, Plateforme de Production de protéines recombinantes, 25 rue du Dr Roux, 75724 Paris Cedex 15, France,

    Christine Girard-Blanc & Elodie Crublet

  6. CNRS URA 2185, 25 rue du Dr Roux, 75724 Paris Cedex 15, France ,

    Christine Girard-Blanc & Elodie Crublet

  7. Synchrotron SOLEIL, L’Orme de Merisiers, BP 48 St Aubin, 91192 Gif sur Yvette, France ,

    Andrew Thompson

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Contributions

J.E.V. made the constructs, produced and purified the protein, grew the crystals and participated in diffraction data collection; analysed the literature and prepared tables and figures. M.-C.V. carried out most of the various crystallographic refinements and prepared the figures, S.D. carried out the fitting into the cryo-EM maps of various alphavirus particles and prepared the figures, C.G.-B. and E.C. participated in optimizing protein production in large scale for crystal trials, C.V. and G.B. participated in data processing and in the structure determination. A.T. carried out specific data collection strategies to improve the signal to noise to extract anomalous signal for phasing; F.A.R. conceived the experiments and wrote the manuscript.

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Correspondence to Félix A. Rey.

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Supplementary information

Supplementary Information

The file contains Supplementary Analysis, Supplementary References, Supplementary Tables 1-7 and Supplementary Figures 1-7 with legends. (ZIP 12830 kb)

Supplementary Movie 1

This movie shows Six spikes around a Q6 axis of the T=4 icosahedral lattice (see legend in Supplementary Information). (MOV 4582 kb)

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Voss, J., Vaney, MC., Duquerroy, S. et al. Glycoprotein organization of Chikungunya virus particles revealed by X-ray crystallography. Nature 468, 709–712 (2010). https://doi.org/10.1038/nature09555

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