Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion

Proceedings of the National Academy of Sciences of the United States of America

Volumn 114, Issue 42, 2017, Pages 11157-11162

  Walls, Alexandra C ^a   Tortorici, M Alejandra ^b,c   Snijder, Joost ^a   Xiong, Xiaoli ^a   Bosch, Berend Jan ^d   Rey, Felix A ^b,c   Veesler, David ^a  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b INSTITUT PASTEUR   (France)

^c Institut Pasteur   (France)

^d UTRECHT UNIVERSITY   (Netherlands)

Author keywords

Coronavirus; CryoEM; Fusion proteins; Membrane fusion; Proteolytic activation

Indexed keywords

GLYCOPROTEIN; INFLUENZA VIRUS HEMAGGLUTININ; SUBUNIT VACCINE; VIRUS FUSION PROTEIN; VITRONECTIN; CORONAVIRUS SPIKE GLYCOPROTEIN;

ARTICLE; BIOCHEMICAL ANALYSIS; COMPARATIVE STUDY; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CORONAVIRIDAE; MASS SPECTROMETRY; MEMBRANE FUSION; MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS; MOLECULAR BIOLOGY; NONHUMAN; PARAMYXOVIRIDAE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN REFOLDING; SARS CORONAVIRUS; VIRUS MORPHOLOGY; ANIMAL; CHEMISTRY; CRYOELECTRON MICROSCOPY; DROSOPHILA; GENETICS; HEK293 CELL LINE; HUMAN; METABOLISM; MUTATION; PROTEIN CONFORMATION; VALIDATION STUDY;

ANIMALS; CRYOELECTRON MICROSCOPY; DROSOPHILA; HEK293 CELLS; HUMANS; MASS SPECTROMETRY; MEMBRANE FUSION; MUTATION; PROTEIN CONFORMATION; SPIKE GLYCOPROTEIN, CORONAVIRUS;

EID: 85031329007     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1708727114     Document Type: Article

References (64)

1. Ge XY, et al. (2013) Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature 503:535–538.
2. Sabir JS, et al. (2016) Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia. Science 351:81–84.
3. Wang Q, et al. (2014) Bat origins of MERS-CoV supported by bat coronavirus HKU4 usage of human receptor CD26. Cell Host Microbe 16:328–337.
4. Yang Y, et al. (2015) Two mutations were critical for bat-to-human transmission of Middle East respiratory syndrome coronavirus. J Virol 89:9119–9123.
5. Bosch BJ, van der Zee R, de Haan CA, Rottier PJ (2003) 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.
6. Walls AC, et al. (2016) Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer. Nature 531:114–117.
7. Walls AC, et al. (2016) Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy. Nat Struct Mol Biol 23:899–905.
8. Gui M, et al. (2017) Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding. Cell Res 27:119–129.
9. Kirchdoerfer RN, et al. (2016) Pre-fusion structure of a human coronavirus spike protein. Nature 531:118–121.
10. Yuan Y, et al. (2017) Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains. Nat Commun 8:15092.
11. Pallesen J, et al. (2017) Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen. Proc Natl Acad Sci USA 114:E7348–E7357.
12. Millet JK, Whittaker GR (2014) Host cell entry of Middle East respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein. Proc Natl Acad Sci USA 111:15214–15219.
13. Belouzard S, Chu VC, Whittaker GR (2009) Activation of the SARS coronavirus spike protein via sequential proteolytic cleavage at two distinct sites. Proc Natl Acad Sci USA 106:5871–5876.
14. Duquerroy S, Vigouroux A, Rottier PJ, Rey FA, Bosch BJ (2005) Central ions and lateral asparagine/glutamine zippers stabilize the post-fusion hairpin conformation of the SARS coronavirus spike glycoprotein. Virology 335:276–285.
15. Supekar VM, et al. (2004) Structure of a proteolytically resistant core from the severe acute respiratory syndrome coronavirus S2 fusion protein. Proc Natl Acad Sci USA 101:17958–17963.
16. Xu Y, et al. (2004) Structural basis for coronavirus-mediated membrane fusion. Crystal structure of mouse hepatitis virus spike protein fusion core. J Biol Chem 279:30514–30522.
17. McLellan JS, et al. (2013) Structure-based design of a fusion glycoprotein vaccine for respiratory syncytial virus. Science 342:592–598.
18. McLellan JS, et al. (2013) Structure of RSV fusion glycoprotein trimer bound to a prefusion-specific neutralizing antibody. Science 340:1113–1117.
19. McLellan JS, Yang Y, Graham BS, Kwong PD (2011) Structure of respiratory syncytial virus fusion glycoprotein in the postfusion conformation reveals preservation of neutralizing epitopes. J Virol 85:7788–7796.
20. Millet JK, Whittaker GR (2015) Host cell proteases: Critical determinants of coronavirus tropism and pathogenesis. Virus Res 202:120–134.
21. Bosch BJ, Bartelink W, Rottier PJ (2008) Cathepsin L functionally cleaves the severe acute respiratory syndrome coronavirus class I fusion protein upstream of rather than adjacent to the fusion peptide. J Virol 82:8887–8890.
22. Burkard C, et al. (2014) Coronavirus cell entry occurs through the endo-/lysosomal pathway in a proteolysis-dependent manner. PLoS Pathog 10:e1004502.
23. Yin HS, Paterson RG, Wen X, Lamb RA, Jardetzky TS (2005) Structure of the uncleaved ectodomain of the paramyxovirus (hPIV3) fusion protein. Proc Natl Acad Sci USA 102:9288–9293.
24. Swanson KA, et al. (2011) Structural basis for immunization with postfusion respiratory syncytial virus fusion F glycoprotein (RSV F) to elicit high neutralizing antibody titers. Proc Natl Acad Sci USA 108:9619–9624.
25. Chen L, et al. (2001) The structure of the fusion glycoprotein of Newcastle disease virus suggests a novel paradigm for the molecular mechanism of membrane fusion. Structure 9:255–266.
26. Li F, et al. (2006) Conformational states of the severe acute respiratory syndrome coronavirus spike protein ectodomain. J Virol 80:6794–6800.
27. Walls A, et al. (2017) Crucial steps in the structure determination of a coronavirus spike glycoprotein using cryo-electron microscopy. Protein Sci 26:113–121.
28. Brown A, et al. (2015) Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions. Acta Crystallogr D Biol Crystallogr 71:136–153.
29. Wang RY, et al. (2015) De novo protein structure determination from near-atomic-resolution cryo-EM maps. Nat Methods 12:335–338.
30. Frenz B, Walls AC, Egelman EH, Veesler D, DiMaio F (2017) RosettaES: A sampling strategy enabling automated interpretation of difficult cryo-EM maps. Nat Methods 14:797–800.
31. DiMaio F, et al. (2015) Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement. Nat Methods 12:361–365.
32. Frese CK, et al. (2013) Unambiguous phosphosite localization using electron-transfer/ higher-energy collision dissociation (EThcD). J Proteome Res 12:1520–1525.
33. Madu IG, Roth SL, Belouzard S, Whittaker GR (2009) Characterization of a highly conserved domain within the severe acute respiratory syndrome coronavirus spike protein S2 domain with characteristics of a viral fusion peptide. J Virol 83:7411–7421.
34. Daniel C, et al. (1993) Identification of an immunodominant linear neutralization domain on the S2 portion of the murine coronavirus spike glycoprotein and evidence that it forms part of complex tridimensional structure. J Virol 67:1185–1194.
35. Zhang H, et al. (2004) Identification of an antigenic determinant on the S2 domain of the severe acute respiratory syndrome coronavirus spike glycoprotein capable of inducing neutralizing antibodies. J Virol 78:6938–6945.
36. Ingallinella P, et al. (2004) Structural characterization of the fusion-active complex of severe acute respiratory syndrome (SARS) coronavirus. Proc Natl Acad Sci USA 101:8709–8714.
37. Krueger DK, Kelly SM, Lewicki DN, Ruffolo R, Gallagher TM (2001) Variations in disparate regions of the murine coronavirus spike protein impact the initiation of membrane fusion. J Virol 75:2792–2802.
38. Taguchi F, Matsuyama S (2002) Soluble receptor potentiates receptor-independent infection by murine coronavirus. J Virol 76:950–958.
39. Yin HS, Wen X, Paterson RG, Lamb RA, Jardetzky TS (2006) Structure of the para-influenza virus 5 F protein in its metastable, prefusion conformation. Nature 439:38–44.
40. Bullough PA, Hughson FM, Skehel JJ, Wiley DC (1994) Structure of influenza hae-magglutinin at the pH of membrane fusion. Nature 371:37–43.
41. Buzon V, et al. (2010) Crystal structure of HIV-1 gp41 including both fusion peptide and membrane proximal external regions. PLoS Pathog 6:e1000880.
42. Weissenhorn W, Carfí A, Lee KH, Skehel JJ, Wiley DC (1998) Crystal structure of the Ebola virus membrane fusion subunit, GP2, from the envelope glycoprotein ectodomain. Mol Cell 2:605–616.
43. Liu Q, et al. (2013) Unraveling a three-step spatiotemporal mechanism of triggering of receptor-induced Nipah virus fusion and cell entry. PLoS Pathog 9:e1003770.
44. Rockx B, et al. (2008) Structural basis for potent cross-neutralizing human monoclonal antibody protection against lethal human and zoonotic severe acute respiratory syndrome coronavirus challenge. J Virol 82:3220–3235.
45. Pascal KE, et al. (2015) Pre- and postexposure efficacy of fully human antibodies against Spike protein in a novel humanized mouse model of MERS-CoV infection. Proc Natl Acad Sci USA 112:8738–8743.
46. Elshabrawy HA, Coughlin MM, Baker SC, Prabhakar BS (2012) Human monoclonal antibodies against highly conserved HR1 and HR2 domains of the SARS-CoV spike protein are more broadly neutralizing. PLoS One 7:e50366.
47. Routledge E, Stauber R, Pfleiderer M, Siddell SG (1991) Analysis of murine coronavirus surface glycoprotein functions by using monoclonal antibodies. J Virol 65:254–262.
48. Zheng SQ, et al. (2017) MotionCor2: Anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat Methods 14:331–332.
49. Kimanius D, Forsberg BO, Scheres SH, Lindahl E (2016) Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2. Elife 5:e18722.
50. Eckert DM, Malashkevich VN, Kim PS (1998) Crystal structure of GCN4-pIQI, a trimeric coiled coil with buried polar residues. J Mol Biol 284:859–865.
51. Berrow NS, et al. (2007) A versatile ligation-independent cloning method suitable for high-throughput expression screening applications. Nucleic Acids Res 35:e45.
52. Suloway C, et al. (2005) Automated molecular microscopy: The new Leginon system. J Struct Biol 151:41–60.
53. Voss NR, Yoshioka CK, Radermacher M, Potter CS, Carragher B (2009) DoG Picker and TiltPicker: Software tools to facilitate particle selection in single particle electron microscopy. J Struct Biol 166:205–213.
54. Zhang K (2016) Gctf: Real-time CTF determination and correction. J Struct Biol 193:1–12.
55. Snijder J, et al. (2017) Vitrification after multiple rounds of sample application and blotting improves particle density on cryo-electron microscopy grids. J Struct Biol 198:38–42.
56. Li X, et al. (2013) Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat Methods 10:584–590.
57. Roseman AM (2004) FindEM–A fast, efficient program for automatic selection of particles from electron micrographs. J Struct Biol 145:91–99.
58. Lander GC, et al. (2009) Appion: An integrated, database-driven pipeline to facilitate EM image processing. J Struct Biol 166:95–102.
59. Goddard TD, Huang CC, Ferrin TE (2007) Visualizing density maps with UCSF Chimera. J Struct Biol 157:281–287.
60. Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66:486–501.
61. DiMaio F, Leaver-Fay A, Bradley P, Baker D, André I (2011) Modeling symmetric macromolecular structures in Rosetta3. PLoS One 6:e20450.
62. DiMaio F, Zhang J, Chiu W, Baker D (2013) Cryo-EM model validation using independent map reconstructions. Protein Sci 22:865–868.
63. Chen VB, et al. (2010) MolProbity: All-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66:12–21.
64. Bern M, Kil YJ, Becker C (2012) Byonic: Advanced peptide and protein identification software. Curr Protoc Bioinformatics Chapter 13:Unit13 20.