Conceptualization, C.-L.H. and J.S.M.; Investigation and visualization, C.-L.H., J.A.G., C.-W.C., A.M.D., K.J., H.-C.K., K.C.L., A.G.-W.L., Y.L., J.M.S., D.W., P.O.B., C.K.H., N.V.J., J.L.-M., A.W.N., J.P., and D.A.; Writing – Original Draft, C.-L.H., J.A.G., D.W., P.O.B., C.K.H., N.V.J., and J.S.M; Writing - Reviewing & Editing, C.-L.H., J.A.G., D.W., P.O.B., N.W., C.K.H., N.V.J., J.A.M., I.J.F., and J.S.M.; Supervision, J.A.M., I.J.F. and J.S.M.

^{Correspondence:}ude.saxetu.ehc@dranyam, gro.balnietsleknif@ayli, ude.saxetu.nitsua@nallelcmj

It is made available under a CC-BY-NC-ND 4.0 International license.

Footnotes

COMPETING INTERESTS

N.W. and J.S.M. are inventors on U.S. patent application no. 62/412,703 (“Prefusion Coronavirus Spike Proteins and Their Use”). D.W., N.W. and J.S.M. are inventors on U.S. patent application no. 62/972,886 (“2019-nCoV Vaccine”). C.-L.H., J.A.G., J.M.S., C.-W.C., A.M.D., K.J., H.-C.K., D.W., P.O.B., C.K.H., N.V.J., N.W., J.A.M., I.J.F., and J.S.M. are inventors on U.S. patent application no. 63/032,502 (“Engineered Coronavirus Spike (S) Protein and Methods of Use Thereof”).

REFERENCES

References

1. Peiris J. S. M. et al. Coronavirus as a possible cause of severe acute respiratory syndrome. Lancet361, 1319–1325 (2003).
2. Zaki A. M., Van Boheemen S., Bestebroer T. M., Osterhaus A. D. M. E. & Fouchier R. A. M. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N. Engl. J. Med.367, 1814–1820 (2012). [[PubMed]
3. Chan J. F. W. et al. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet395, 514–523 (2020).
4. Huang C. et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet395, 497–506 (2020).
5. Li F. Structure, Function, and Evolution of Coronavirus Spike Proteins. Annu. Rev. Virol.3, 237–261 (2016).
6. Siebert D. N., Bosch B. J., van der Zee R., de Haan C. A. M. & Rottier P. J. M. The Coronavirus Spike Protein Is a Class I Virus Fusion Protein: Structural and Functional Characterization of the Fusion Core Complex. J. Virol.77, 8801–8811 (2003).
7. Mille J. K. & Whittaker G. R. Host cell entry of Middle East respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein. Proc. Natl. Acad. Sci. U. S. A.111, 15214–15219 (2014).
8. Hoffmann M. et al. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell181, 271–280.e8 (2020).
9. Wan Y., Shang J., Graham R., Baric R. S. & Li F. Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus. J. Virol.94, 1–9 (2020).
10. Zhou P. et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature579, 270–273 (2020).
11. Walls AC. et al. Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion. Proc. Natl. Acad. Sci. U. S. A.114, 11157–11162 (2017). [Google Scholar]
12. Buchholz UJ. et al. Contributions of the structural proteins of severe respiratory syndrome coronavirus to protective immunity. Proc. Natl. Acad. Sci. U. S. A.101, 9804–9809 (2004). [Google Scholar]
13. Hofmann H. et al. S Protein of Severe Acute Respiratory Syndrome-Associated Coronavirus Mediates Entry into Hepatoma Cell Lines and Is Targeted by Neutralizing Antibodies in Infected Patients. J. Virol.78, 6134–6142 (2004).
14. Sanders RW. et al. A next-generation cleaved, soluble HIV-1 Env trimer, BG505 SOSIP.664 gp140, expresses multiple epitopes for broadly neutralizing but not non-neutralizing antibodies. PLoS Pathog.9, e1003618 (2013). [Google Scholar]
15. Pallesen J. et al. Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen. Proc. Natl. Acad. Sci. U. S. A.114, E7348–E7357 (2017).
16. Crank MC. et al. A proof of concept for structure-based vaccine design targeting RSV in humans. Science (80-. ).365, 505–509 (2019). [[PubMed][Google Scholar]
17. Park YJ. et al. Structures of MERS-CoV spike glycoprotein in complex with sialoside attachment receptors. Nat. Struct. Mol. Biol.26, 1151–1157 (2019). [Google Scholar]
18. Li Z. et al. The human coronavirus HCoV-229E S-protein structure and receptor binding. Elife8, 1–22 (2019).
19. Wang N. et al. Structural Definition of a Neutralization-Sensitive Epitope on the MERSCoV S1-NTD. Cell Rep. 28, 3395–3405.e6 (2019).
20. Walls AC. et al. Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion. Cell176, 1026–1039.e15 (2019). [Google Scholar]
21. Wrapp D. et al. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science (80-. ).367, 1260–1263 (2020).
22. Walls AC. et al. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell181, 281–292.e6 (2020). [Google Scholar]
23. McLellan JS. et al. Structure-based design of a fusion glycoprotein vaccine for respiratory syncytial virus. Science342, 592–598 (2013). [Google Scholar]
24. Rutten L. et al. A Universal Approach to Optimize the Folding and Stability of Prefusion-Closed HIV-1 Envelope Trimers. Cell Rep.23, 584–595 (2018).
25. Yang L. et al. Structure-Guided Redesign Improves NFL HIV Env Trimer Integrity and Identifies an Inter-Protomer Disulfide Permitting Post-Expression Cleavage. Front. Immunol.9, 1631 (2018).
26. Joyce MG. et al. Iterative structure-based improvement of a fusion-glycoprotein vaccine against RSV. Nat. Struct. Mol. Biol.23, 811–820 (2016). [Google Scholar]
27. Krarup A. et al. A highly stable prefusion RSV F vaccine derived from structural analysis of the fusion mechanism. Nat. Commun.6, 8143 (2015).
28. Rutten L. et al. Structure-Based Design of Prefusion-Stabilized Filovirus Glycoprotein Trimers. Cell Rep.30, 4540–4550.e3 (2020).
29. Battles MB. et al. Structure and immunogenicity of pre-fusion-stabilized human metapneumovirus F glycoprotein. Nat. Commun.8, 1528 (2017). [Google Scholar]
30. Qiao H. et al. Specific single or double proline substitutions in the ‘spring-loaded’ coiled-coil region of the influenza hemagglutinin impair or abolish membrane fusion activity. J. Cell Biol.141, 1335–1347 (1998).
31. Hastie KM. et al. Structural basis for antibody-mediated neutralization of Lassa virus. Science (80-. ).356, 923–928 (2017). [Google Scholar]
32. Impagliazzo A. et al. A stable trimeric influenza hemagglutinin stem as a broadly protective immunogen. Science349, 1301–1306 (2015). [[PubMed]
33. Henderson R. et al. Controlling the SARS-CoV-2 Spike Glycoprotein Conformation. bioRxiv 2020.05.18.102087 (2020). doi:10.1101/2020.05.18.102087 [[PubMed]
34. Tegunov D& Cramer P. Real-time cryo-electron microscopy data preprocessing with Warp. Nat. Methods16, 1146–1152 (2019). [Google Scholar]
35. Punjani A., Rubinstein J. L., Fleet D. J. & Brubaker M. A. CryoSPARC: Algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods14, 290–296 (2017). [[PubMed]
36. Ramírez-Aportela E. et al. Automatic local resolution-based sharpening of cryo-EM maps. Bioinformatics36, 765–772 (2020). [[PubMed]
37. Emsley P., Lohkamp B., Scott W. G. & Cowtan K. Features and development of Coot. Acta Crystallogr. D. Biol. Crystallogr.66, 486–501 (2010).
38. Liebschner D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: Recent developments in Phenix. Acta Crystallogr. Sect. D Struct. Biol.75, 861–877 (2019).
39. Croll TI. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. Sect. D, Struct. Biol.74, 519–530 (2018). [Google Scholar]