Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Structure of the immature Zika virus at 9 Å resolution

Abstract

The current Zika virus (ZIKV) epidemic is characterized by severe pathogenicity in both children and adults. Sequence changes in ZIKV since its first isolation are apparent when pre-epidemic strains are compared with those causing the current epidemic. However, the residues that are responsible for ZIKV pathogenicity are largely unknown. Here we report the cryo-electron microscopy (cryo-EM) structure of the immature ZIKV at 9-Å resolution. The cryo-EM map was fitted with the crystal structures of the precursor membrane and envelope glycoproteins and was shown to be similar to the structures of other known immature flaviviruses. However, the immature ZIKV contains a partially ordered capsid protein shell that is less prominent in other immature flaviviruses. Furthermore, six amino acids near the interface between pr domains at the top of the spikes were found to be different between the pre-epidemic and epidemic ZIKV, possibly influencing the composition and structure of the resulting viruses.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Cryo-EM structure of immature Zika virus.
Figure 2: Cross-section of the immature ZIKV contoured to show the inner capsid shell.
Figure 3: Interface between prM–E heterodimers.

Similar content being viewed by others

Accession codes

Primary accessions

Electron Microscopy Data Bank

Protein Data Bank

Referenced accessions

Protein Data Bank

References

  1. Schuler-Faccini, L. et al. Possible association between Zika virus infection and microcephaly - Brazil, 2015. MMWR Morb. Mortal. Wkly. Rep. 65, 59–62 (2016).

    Article  Google Scholar 

  2. Chan, J.F., Choi, G.K., Yip, C.C., Cheng, V.C. & Yuen, K.Y. Zika fever and congenital Zika syndrome: An unexpected emerging arboviral disease. J. Infect. 72, 507–524 (2016).

    Article  Google Scholar 

  3. Lindenbach, B.D., Murray, C.L., Thiel, H.-J. & Rice, C.M. Fields Virology (eds. Knipe, D.M. et al.) (Lippincott Williams & Wilkins, 2013).

  4. Mukhopadhyay, S., Kuhn, R.J. & Rossmann, M.G. A structural perspective of the flavivirus life cycle. Nat. Rev. Microbiol. 3, 13–22 (2005).

    Article  CAS  Google Scholar 

  5. Kuhn, R.J. et al. Structure of dengue virus: implications for flavivirus organization, maturation, and fusion. Cell 108, 717–725 (2002).

    Article  CAS  Google Scholar 

  6. Mukhopadhyay, S., Kim, B.S., Chipman, P.R., Rossmann, M.G. & Kuhn, R.J. Structure of West Nile virus. Science 302, 248 (2003).

    Article  CAS  Google Scholar 

  7. Zhang, X. et al. Cryo-EM structure of the mature dengue virus at 3.5-Å resolution. Nat. Struct. Mol. Biol. 20, 105–110 (2013).

    Article  Google Scholar 

  8. Sirohi, D. et al. The 3.8 Å resolution cryo-EM structure of Zika virus. Science 352, 467–470 (2016).

    Article  CAS  Google Scholar 

  9. Kostyuchenko, V.A. et al. Structure of the thermally stable Zika virus. Nature 533, 425–428 (2016).

    Article  CAS  Google Scholar 

  10. Zhang, Y. et al. Structures of immature flavivirus particles. EMBO J. 22, 2604–2613 (2003).

    Article  CAS  Google Scholar 

  11. Stadler, K., Allison, S.L., Schalich, J. & Heinz, F.X. Proteolytic activation of tick-borne encephalitis virus by furin. J. Virol. 71, 8475–8481 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Yu, I.-M. et al. Structure of the immature dengue virus at low pH primes proteolytic maturation. Science 319, 1834–1837 (2008).

    Article  CAS  Google Scholar 

  13. Rodenhuis-Zybert, I.A. et al. Immature dengue virus: a veiled pathogen? PLoS Pathog. 6, e1000718 (2010).

    Article  Google Scholar 

  14. Colpitts, T.M. et al. prM-antibody renders immature West Nile virus infectious in vivo. J. Gen. Virol. 92, 2281–2285 (2011).

    Article  CAS  Google Scholar 

  15. Li, L. et al. The flavivirus precursor membrane-envelope protein complex: structure and maturation. Science 319, 1830–1834 (2008).

    Article  CAS  Google Scholar 

  16. Kostyuchenko, V.A., Zhang, Q., Tan, J.L., Ng, T.S. & Lok, S.M. Immature and mature dengue serotype 1 virus structures provide insight into the maturation process. J. Virol. 87, 7700–7707 (2013).

    Article  CAS  Google Scholar 

  17. Ma, L., Jones, C.T., Groesch, T.D., Kuhn, R.J. & Post, C.B. Solution structure of dengue virus capsid protein reveals another fold. Proc. Natl. Acad. Sci. USA 101, 3414–3419 (2004).

    Article  CAS  Google Scholar 

  18. Dokland, T. et al. West Nile virus core protein; tetramer structure and ribbon formation. Structure 12, 1157–1163 (2004).

    Article  CAS  Google Scholar 

  19. Wang, L. et al. From mosquitos to humans: genetic evolution of Zika virus. Cell Host Microbe 19, 561–565 (2016).

    Article  CAS  Google Scholar 

  20. Pierson, T.C. et al. The stoichiometry of antibody-mediated neutralization and enhancement of West Nile virus infection. Cell Host Microbe 1, 135–145 (2007).

    Article  CAS  Google Scholar 

  21. Nelson, S. et al. Maturation of West Nile virus modulates sensitivity to antibody-mediated neutralization. PLoS Pathog. 4, e1000060 (2008).

    Article  Google Scholar 

  22. Davenport, T.M. et al. Isolate-specific differences in the conformational dynamics and antigenicity of HIV-1 gp120. J. Virol. 87, 10855–10873 (2013).

    Article  CAS  Google Scholar 

  23. Kwong, P.D. et al. HIV-1 evades antibody-mediated neutralization through conformational masking of receptor-binding sites. Nature 420, 678–682 (2002).

    Article  CAS  Google Scholar 

  24. Dejnirattisai, W. et al. Dengue virus sero-cross-reactivity drives antibody-dependent enhancement of infection with Zika virus. Nat. Immunol. 17, 1102–1108 (2016).

    Article  CAS  Google Scholar 

  25. Tirado, S.M. & Yoon, K.J. Antibody-dependent enhancement of virus infection and disease. Viral Immunol. 16, 69–86 (2003).

    Article  CAS  Google Scholar 

  26. Tang, G. et al. EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38–46 (2007).

    Article  CAS  Google Scholar 

  27. Scheres, S.H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).

    Article  CAS  Google Scholar 

  28. Guo, F. & Jiang, W. Single particle cryo-electron microscopy and 3-D reconstruction of viruses. Methods Mol. Biol. 1117, 401–443 (2014).

    Article  CAS  Google Scholar 

  29. Pettersen, E.F. et al. UCSF Chimera--a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

    Article  CAS  Google Scholar 

  30. Katoh, K. & Standley, D.M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).

    Article  CAS  Google Scholar 

  31. Robert, X. & Gouet, P. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res. 42, W320–W324 (2014).

    Article  CAS  Google Scholar 

  32. Pickett, B.E. et al. ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res. 40, D593–D598 (2012).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank M. Sevvana for discussions about the manuscript. We thank S. Kelly for helping us prepare the manuscript. We also thank the Purdue Cryo-EM Facility for equipment access and support. This work was supported by the National Institutes of Health (RO1 AI076331 to M.G.R. and R.J.K., and a subaward for RO1 AI073755 (principal investigator: M.S. Diamond, Washington University) to both M.G.R. and R.J.K.).

Author information

Authors and Affiliations

Authors

Contributions

A.S.M., D.S. and G.B. were involved in preparation of cell culture, and optimization and purification of virus sample; V.M.P. and T.K. conducted the cryo-EM preparation, data collection and data processing; V.M.P. performed the data analyses; W.J. made his JSPR program available for reconstruction and refinement of the cryo-EM map; and V.M.P., R.J.K. and M.G.R. wrote the paper.

Corresponding authors

Correspondence to Richard J Kuhn or Michael G Rossmann.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Resolution estimation using Fourier shell correlation (FSC).

A plot of FSC against resolution in Å-1, calculated using two independent half-sets of the cryo-EM data. The resolution of the map is 9.1 Å using the 0.143 FSC cut-off (light blue line).

Supplementary Figure 2 Fit of the DENV-2 prM–E crystal structure into the immature ZIKV cryo-EM map.

a, Surface view of the complete immature ZIKV. One of the 60 trimeric spikes is identified in color, with its E proteins in green and the pr domains in orange. The asymmetric unit is shown as a black triangle. The scale bar is 100 Å long. b, Top view showing the fit of three prM-E heterodimers into the cryo-EM spike density. The three independent prM-E heterodimers are colored in light green, blue and orange for the E proteins and dark green, dark blue and red for the pr domains, respectively. c, Side-view of the fitted prM-E heterodimers in a spike. The dashed black line shows the position of the viral membrane surface. d, Cryo-EM density showing the individual fitting of the transmembrane regions of E (blue) and M (magenta) proteins. Scale bar is 50 Å long in b, c and d.

Supplementary Figure 3 Analysis of crystal structures fitted into immature ZIKV cryo-EM map.

a, Cryo-EM density showing the conservation of Asn-69 glycosylation site in the pr domains of immature ZIKV. The DENV-2 prM-E crystal structure (PDB ID: 3C6E) including the Asn-69 glycan has been fitted into all three positions within a trimeric spike. The glycans attached to Asn-69 are shown in blue. Scale bar is 25 Å in length. b, Glycan (colored in blue) attached to Asn-67 in the DENV-2 E protein structure and fitted into the map of the immature ZIKV showing the absence of density associated with the glycan at this site in ZIKV. c, Additional density adjacent to Asn-154 (red) in immature ZIKV indicating the presence of a glycan. Scale bar is 10 Å long in b and c. Black arrows in a and c point to the densities of the glycans. The E proteins and pr domains are shown in green and orange respectively in all panels.

Supplementary Figure 4 Alignment of sequences that form the interfaces between immature ZIKV spikes.

Top panel, Alignment of pr domain sequences from different flaviviruses. The residues that differ between the pre-epidemic (African) and epidemic (Asian) ZIKV strains are indicated in blue boxes. Bottom panel, Alignment of parts of the E protein sequence from different flaviviruses. In both panels, red columns indicate strictly conserved residues, yellow columns show partially conserved residues and white columns show variable residues. Residues involved in interactions within a trimeric spike and between adjacent spikes are indicated by brown and green colored bars above the corresponding residues, respectively. The furin cleavage site at the end of the pr domain is shown by a grey bar. Abbreviations DEN, JEV and YFV refer to dengue virus, Japanese encephalitis virus and yellow fever virus respectively.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–4 and Supplementary Table 1 (PDF 1060 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Prasad, V., Miller, A., Klose, T. et al. Structure of the immature Zika virus at 9 Å resolution. Nat Struct Mol Biol 24, 184–186 (2017). https://doi.org/10.1038/nsmb.3352

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue date:

  • DOI: https://doi.org/10.1038/nsmb.3352

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing