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Structural basis for dsRNA recognition and interferon antagonism by Ebola VP35

Abstract

Ebola viral protein 35 (VP35), encoded by the highly pathogenic Ebola virus, facilitates host immune evasion by antagonizing antiviral signaling pathways, including those initiated by RIG-I–like receptors. Here we report the crystal structure of the Ebola VP35 interferon inhibitory domain (IID) bound to short double-stranded RNA (dsRNA), which together with in vivo results reveals how VP35-dsRNA interactions contribute to immune evasion. Conserved basic residues in VP35 IID recognize the dsRNA backbone, whereas the dsRNA blunt ends are 'end-capped' by a pocket of hydrophobic residues that mimic RIG-I–like receptor recognition of blunt-end dsRNA. Residues critical for RNA binding are also important for interferon inhibition in vivo but not for viral polymerase cofactor function of VP35. These results suggest that simultaneous recognition of dsRNA backbone and blunt ends provides a mechanism by which Ebola VP35 antagonizes host dsRNA sensors and immune responses.

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Figure 1: Overall structure of the VP35 IID–dsRNA complex.
Figure 2: Conserved basic residues are important for protein-protein and protein-dsRNA interactions.
Figure 3: The VP35 IID central basic patch residues are critical for dsRNA recognition.
Figure 4: Intersubdomain interface of VP35 IID forms an end cap that recognizes blunt ends of duplex RNA.
Figure 5: Residues from the central basic patch and the end cap of VP35 IID play key roles in the IFN-antagonist function.
Figure 6: VP35 competes with RIG-I for dsRNA binding and inhibits RIG-I–dependent IFN-β promoter activation by dsRNA.

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Acknowledgements

We thank the Iowa State University Biotechnology Facilities and J. Hoy, N. Pohl and D.B. Fulton for providing access to instrumentation and support. We also thank M. Nilsen-Hamilton and M. Shogren-Knaak for discussions, J. Binning, C. Brown and T. Wang for reading the manuscript, L. Tantral and D. Peterson for lab assistance and S. Ginnell, N. Duke, F. Rotella, M. Cuff and J. Lazarz at Advanced Photon Source Sector 19. Use of the Argonne National Laboratory Structural Biology Center beamlines at the Advanced Photon Source was supported by the US Department of Energy under contract DE-AC02-06CH11357. This work is supported by US National Institutes of Health grants (1F32AI084324 to D.W.L., R01GM053163 to Z.O., R01NS010546 to R.B.H., R01AI059536 and AI057158 (Northeast Biodefense Center-Lipkin) to C.F.B. and R01AI081914 to G.K.A.), a Midwest Regional Center of Excellence Developmental grant (U54AI057160-Virgin(PI) to G.K.A.) and the Roy J. Carver Charitable Trust (09-3271 to G.K.A.).

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D.W.L., C.F.B. and G.K.A. designed research; D.W.L., K.C.P., D.M.B., M.F., J.M.T., P.R., J.C.N., L.A.H., Z.O., R.B.H., C.F.B. and G.K.A. performed research and analyzed data; D.W.L., K.C.P., C.F.B. and G.K.A. wrote the manuscript.

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Correspondence to Gaya K Amarasinghe.

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Iowa State University has submitted a provisional patent application on the “Crystal Structure of Ebola VP35 Protein and Methods of Use.”

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Leung, D., Prins, K., Borek, D. et al. Structural basis for dsRNA recognition and interferon antagonism by Ebola VP35. Nat Struct Mol Biol 17, 165–172 (2010). https://doi.org/10.1038/nsmb.1765

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