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Functional and evolutionary insight from the crystal structure of rubella virus protein E1

Nature volume 493, pages 552–556 (2013)Cite this article

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Abstract

Little is known about the three-dimensional organization of rubella virus, which causes a relatively mild measles-like disease in children but leads to serious congenital health problems when contracted in utero1. Although rubella virus belongs to the same family as the mosquito-borne alphaviruses, in many respects it is more similar to other aerosol-transmitted human viruses such as the agents of measles and mumps. Although the use of the triple MMR (measles, mumps and rubella) live vaccine has limited its incidence in western countries, congenital rubella syndrome remains an important health problem in the developing world. Here we report the 1.8 Å resolution crystal structure of envelope glycoprotein E1, the main antigen and sole target of neutralizing antibodies against rubella virus. E1 is the main player during entry into target cells owing to its receptor-binding and membrane-fusion functions. The structure reveals the epitope and the neutralization mechanism of an important category of protecting antibodies against rubella infection. It also shows that rubella virus E1 is a class II fusion protein, which had hitherto only been structurally characterized for the arthropod-borne alphaviruses and flaviviruses. In addition, rubella virus E1 has an extensive membrane-fusion surface that includes a metal site, reminiscent of the T-cell immunoglobulin and mucin family of cellular proteins that bind phosphatidylserine lipids at the plasma membrane of cells undergoing apoptosis. Such features have not been seen in any fusion protein crystallized so far. Structural comparisons show that the class II fusion proteins from alphaviruses and flaviviruses, despite belonging to different virus families, are closer to each other than they are to rubella virus E1. This suggests that the constraints on arboviruses imposed by alternating cycles between vertebrates and arthropods resulted in more conservative evolution. By contrast, in the absence of this constraint, the strictly human rubella virus seems to have drifted considerably into a unique niche as sole member of the Rubivirus genus.

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Figure 1: Negative-stain electron microscopy observations of E1e trimers in isolation and bound to liposomes.
Figure 2: Crystal structure of rubella virus E1e.
Figure 3: Metal and pH dependence of liposome binding.

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Primary accessions

Protein Data Bank

Data deposits

The atomic coordinates and structure factors have been deposited in the Protein Data Bank under accession numbers 4ADI, 4ADG, 4ADJ and 4B3V. They correspond to the atomic models of Na+-bound E1e, Ca2+-bound E1e (from the galactose-3-sulphate headgroup soak (see Supplementary Table 2)), and to E1e crystallized in the presence of calcium acetate at 1 and 20mM, respectively.

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Acknowledgements

We thank A. Haouz of Institut Pasteur and the PXI beam line staff at the Swiss Light Source and PROXIMA 1 beam line at SOLEIL synchrotron facilities for assistance; C. Vonrhein at Global Phasing for expertise in phase determination; G. Bricogne for input, G. Dupras and J.M. Mallet at École Normale Supérieure in Paris for the synthesis of galactose-3-sulphate used in co-crystallization trials; and J. Casasnovas, L. Chernomordik, Y. Gaudin, S. Harrison, F. Heinz, M. Kielian and J. Lepault for discussion. R.M.D. was supported by a ‘Pasteur–Howard’ fellowship. This work was mainly funded by grant ANR-05-MIIM-012-02-Dentry to F.A.R., who also acknowledges support from Merck-Serono from the French Government’s Investissements d’Avenir program: Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (grant no. ANR-10-LABX-62-IBEID).

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Authors and Affiliations

  1. Département de Virologie, Institut Pasteur, Unité de Virologie Structurale and CNRS URA 3015, F-75724 Paris Cedex 15, France,

    Rebecca M. DuBois, Marie-Christine Vaney, M. Alejandra Tortorici, Rana Al Kurdi, Giovanna Barba-Spaeth, Thomas Krey & Félix A. Rey

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Contributions

R.M.D. produced and crystallized E1e. R.M.D. and M.-C.V. solved the E1e structure (with initial help from C. Vonrhein) and participated in manuscript preparation. M.A.T. performed liposome flotation assays and crystallized E1e with calcium acetate. R.A.-K. performed liposome flotation assays and electron microscopy studies. G.B.-S. characterized E1e produced in mammalian cells. T.K. constructed the modified pMT plasmid used for E1e expression. F.A.R. conceived the experiments and wrote the manuscript with R.M.D. and M.C.V.

Corresponding author

Correspondence to Félix A. Rey.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-8, Supplementary Methods, Supplementary Tables 1-2 and Supplementary Results and Discussion. These Supplementary items provide further detail regarding the biochemical and structural features of E1e, including details about the metal-binding site and comparison to other class II viral fusion proteins. (PDF 6782 kb)

The fusion surface

Each subunit is colored according to domains (yellow, red and blue, as above, with the stem region pink/magenta). Domain II is represented in gold and pale yellow, as in figures S4 and S8. The side chains of residues at the fusion surface are drawn as sticks colored according to atom type (carbon white, nitrogen blue, oxygen red). The video initially shows a ribbon diagram of the trimer, and then switches to a full-surface representation (both solid and semitransparent). The conformation displayed is that of calcium acetate bound, as observed in crystal form 2, with the Ca2+ ion represented as a green sphere and the acetate anion as sticks colored according to atom type, with carbon atoms cyan. The sticks in the acetate ion switch to spheres later in the video, so that the acetate can still be seen in the context of the molecular surface of the trimer. The video shows that FL1 and FL2 make a ridge at the edges of a relatively flat surface, rich in aromatic residues, that is exposed to the membrane (termed the “fusion surface”). The three metal ions are on the internal side of the ridges, and the 3 stems end at the opposite side, at the base of the ridges. (MPG 16283 kb)

Conformational change in FL2 upon Ca2+ binding

Transition from Na+-bound to Ca2+-bound conformation and back, generated by morphing one structure into the other to illustrate the change in main chain and side chains in FL2. (MPG 1465 kb)

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DuBois, R., Vaney, MC., Tortorici, M. et al. Functional and evolutionary insight from the crystal structure of rubella virus protein E1. Nature 493, 552–556 (2013). https://doi.org/10.1038/nature11741

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