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Atomic structures of enterovirus D68 in complex with two monoclonal antibodies define distinct mechanisms of viral neutralization

Nature Microbiology volume 4, pages 124–133 (2019)Cite this article

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Abstract

Enterovirus D68 (EV-D68) undergoes structural transformation between mature, cell-entry intermediate (A-particle) and empty forms throughout its life cycle. Structural information for the various forms and antibody-bound capsids will facilitate the development of effective vaccines and therapeutics against EV-D68 infection, which causes childhood respiratory and paralytic diseases worldwide. Here, we report the structures of three EV-D68 capsid states representing the virus at major phases. We further describe two original monoclonal antibodies (15C5 and 11G1) with distinct structurally defined mechanisms for virus neutralization. 15C5 and 11G1 engage the capsid loci at icosahedral three-fold and five-fold axes, respectively. To block viral attachment, 15C5 binds three forms of capsids, and triggers mature virions to transform into A-particles, mimicking engagement by the functional receptor ICAM-5, whereas 11G1 exclusively recognizes the A-particle. Our data provide a structural and molecular explanation for the transition of picornavirus capsid conformations and demonstrate distinct mechanisms for antibody-mediated neutralization.

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Fig. 1: The cryoEM structures of EV-D68 particles.
Fig. 2: Characterization of the neutralizing antibodies 15C5 and 11G1.
Fig. 3: CryoEM structures of immune complexes EV-D68-M:15C5 and EV-D68-A:11G1.
Fig. 4: Superposition of mature virion with or without the binding of 15C5 shows details of 15C5-induced conformational changes.
Fig. 5: The cryoEM structure of EV-D68 in complex with 15C5 and 11G1.

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Data availability

The atomic coordinates of the mature virion, procapsid, A-particle_i5, EV-D68-M:15C5 and EV-D68-M:15C5:11G1 have been deposited in the Protein Data Bank (accession numbers 6AJ0, 6AJ3, 6AJ2, 6AJ7 and 6AJ9, respectively). The cryoEM maps of the mature virion, procapsid, A-particle_us, A-particle_i5, EV-D68-M:15C5, EV-D68-A:11G1 and EV-D68-M:15C5:11G1 have been deposited in the Electron Microscopy Data Bank (accession numbers EMDB-9629, EMDB-9632, EMDB-9635, EMDB-9631, EMDB-9633, EMDB-9636 and EMDB-9634, respectively).

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Acknowledgements

This work was supported by a grant from the National Science and Technology Major Projects for Major New Drugs Innovation and Development (no. 2018ZX09711003-005-003), the National Science and Technology Major Project of Infectious Diseases (no. 2017ZX10304402-002-003), the National Natural Science Foundation of China (no. 81401669 and 81801646) and the Natural Science Foundation of Fujian Province (no. 2015J05073). This work was supported in part by funding by the National Institutes of Health (grants R37-GM33050, GM071940, DE025567 and AI094386). We acknowledge the use of instruments at the Electron Imaging Center for Nanomachines supported by UCLA and by instrumentation grants from the NIH (1S10RR23057 and 1U24GM116792) and NSF (DBI-1338135 and DMR-1548924). The funders had no role in the study design, data collection and analysis, decision to publish or preparation of the manuscript. We also thank L. Wang and K. M. Morabito for proofreading the manuscript.

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Author notes

  1. These authors contributed equally: Qingbing Zheng, Rui Zhu, Longfa Xu, Maozhou He, Xiaodong Yan.

  2. These authors jointly supervised this work: Z. Hong Zhou and Timothy S. Baker.

Authors and Affiliations

  1. State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, School of Public Health, Xiamen University, Xiamen, China

    Qingbing Zheng, Rui Zhu, Longfa Xu, Maozhou He, Xiaodong Yan, Dongxiao Liu, Zhichao Yin, Yangtao Wu, Yongchao Li, Lisheng Yang, Wangheng Hou, Shuxuan Li, Zizhen Li, Zhenqin Chen, Zhihai Li, Hai Yu, Ying Gu, Jun Zhang, Tong Cheng, Shaowei Li & Ningshao Xia

  2. Department of Chemistry and Biochemistry and Division of Biological Sciences, University of California, San Diego, San Diego, CA, USA

    Xiaodong Yan & Timothy S. Baker

  3. The California NanoSystems Institute, UCLA, Los Angeles, CA, USA

    Z. Hong Zhou

  4. Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA

    Z. Hong Zhou

  5. Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA

    Barney S. Graham

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Contributions

N.X., T.C., Shaowei L., B.S.G., L.X. and Q.Z. contributed to experimental design. R.Z., L.X., D.L., Z.Y., Y.W., Y.L. and L.Y. contributed to virus preparation and characteristic analysis. Y.L., W.H. and Shuxuan L. contributed to preparation and in vitro characterization of antibody. R.Z, L.X. and D.L. performed animal experiments. Q.Z., M.H., X.Y., Z.C., Zizhen L., Zhihai L., H.Y. and Y.G. contributed to structural data collection and analysis. Q.Z., R.Z, L.X., M.H. and X.Y. prepared the original manuscript. Shaowei L., T.C., J.Z., Z.H.Z., T.S.B. and B.S.G. approved the final version. All authors discussed the results and commented on the manuscript.

Corresponding authors

Correspondence to Barney S. Graham, Tong Cheng, Shaowei Li or Ningshao Xia.

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Supplementary information

Supplementary Information

Supplementary Figures 1–13, Supplementary Tables 1–4.

Reporting Summary

Supplementary Video 1

Conformational changes of a protomer when EV-D68 mature virion transforms (triggered by ICAM-5) into A-particle.

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Zheng, Q., Zhu, R., Xu, L. et al. Atomic structures of enterovirus D68 in complex with two monoclonal antibodies define distinct mechanisms of viral neutralization. Nat Microbiol 4, 124–133 (2019). https://doi.org/10.1038/s41564-018-0275-7

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