Structural changes of envelope proteins during alphavirus fusion

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Alphaviruses are enveloped RNA viruses that have a diameter of about 700 Å and can be lethal human pathogens1. Entry of virus into host cells by endocytosis is controlled by two envelope glycoproteins, E1 and E2. The E2–E1 heterodimers form 80 trimeric spikes on the icosahedral virus surface1,2, 60 with quasi-three-fold symmetry and 20 coincident with the icosahedral three-fold axes arranged with T = 4 quasi-symmetry. The E1 glycoprotein has a hydrophobic fusion loop at one end and is responsible for membrane fusion3,4. The E2 protein is responsible for receptor binding5,6 and protects the fusion loop at neutral pH. The lower pH in the endosome induces the virions to undergo an irreversible conformational change in which E2 and E1 dissociate and E1 forms homotrimers, triggering fusion of the viral membrane with the endosomal membrane and then releasing the viral genome into the cytoplasm3,4. Here we report the structure of an alphavirus spike, crystallized at low pH, representing an intermediate in the fusion process and clarifying the maturation process. The trimer of E2–E1 in the crystal structure is similar to the spikes in the neutral pH virus except that the E2 middle region is disordered, exposing the fusion loop. The amino- and carboxy-terminal domains of E2 each form immunoglobulin-like folds, consistent with the receptor attachment properties of E2.

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Figure 1: The structural proteins of an alphavirus.
Figure 2: Stereo diagrams showing the trimeric spike structure.
Figure 3: The E2–E1 heterodimer.
Figure 4: Cartoon showing maturation and fusion.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The atomic coordinates of the E2–E1 heterodimer crystal structures have been deposited with the Protein Data Bank (accession number 3MUU). The fit of the E2–E1 heterodimer into the cryo-EM reconstruction of Sindbis virus has been deposited with the Protein Data Bank (accession number 3MUW).


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We wish to thank S. Sun, A. Aksyuk and T. Edwards for discussions. We are also grateful to S. Kelly for help in the preparation of the manuscript. We thank F. Rey for sharing the coordinates of Chikungunya virus E2–E1 to help interpret the Sindbis virus cryo-EM density of the E2 domain B. We would like to thank the staff at the Advanced Photon Source, Argonne National Laboratory, GM/CA sector for their help in data collection. The work was supported by NIH grant P01 AI055672 to R.J.K. and M.G.R.

Author information

L.L. designed the expression constructs, J.J. cloned the constructs, and L.L. and J.J. developed the expression system and purified the protein. L.L. crystallized the protein, collected X-ray diffraction data and, with Y.X., determined the structure. L.L., R.J.K. and M.G.R. discussed the results and wrote the paper.

Correspondence to Michael G. Rossmann.

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Li, L., Jose, J., Xiang, Y. et al. Structural changes of envelope proteins during alphavirus fusion. Nature 468, 705–708 (2010) doi:10.1038/nature09546

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