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The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism

Chen, Nai-Chi and Yoshimura, Masato and Miyazaki, Naoyuki and Guan, Hong-Hsiang and Chuankhayan, Phimonphan and Lin, Chien-Chih and Chen, Shao-Kang and Lin, Pei-Ju and Huang, Yen-Chieh and Iwasaki, Kenji and Nakagawa, Atsushi and Chan, Sunney I. and Chen, Chun-Jung (2019) The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism. Communications Biology, 2 . Art. No. 72. ISSN 2399-3642. PMCID PMC6382870.

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Shrimp nodaviruses, including Penaeus vannamei (PvNV) and Macrobrachium rosenbergii nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity during infections. Here, we show cryo-EM structures of T = 3 and T = 1 PvNV-like particles (PvNV-LPs), crystal structures of the protrusion-domains (P-domains) of PvNV and MrNV, and the crystal structure of the ∆N-ARM-PvNV shell-domain (S-domain) in T = 1 subviral particles. The capsid protein of PvNV reveals five domains: the P-domain with a new jelly-roll structure forming cuboid-like spikes; the jelly-roll S-domain with two calcium ions; the linker between the S- and P-domains exhibiting new cross and parallel conformations; the N-arm interacting with nucleotides organized along icosahedral two-fold axes; and a disordered region comprising the basic N-terminal arginine-rich motif (N-ARM) interacting with RNA. The N-ARM controls T = 3 and T = 1 assemblies. Increasing the N/C-termini flexibility leads to particle polymorphism. Linker flexibility may influence the dimeric-spike arrangement.

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URLURL TypeDescription CentralArticle
Yoshimura, Masato0000-0002-7466-2192
Nakagawa, Atsushi0000-0002-1700-7861
Chan, Sunney I.0000-0002-5348-2723
Chen, Chun-Jung0000-0002-5157-4288
Additional Information:© 2019 The Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit Received 24 August 2018; Accepted 17 January 2019; Published 20 February 2019. Data availability: Coordinates for the cryo-EM and crystal structures of PvNV and MrNV are deposited in the Protein Data Bank under accession codes 6AB5, 6AB6, 5YKU, 5YKV, 5YKX, 5YKZ, 5YL0, and 5YL1. Cryo-EM reconstructions of the T = 3 and T = 1 PvNV-LPs are deposited in the EM Data Bank under accession codes EMD-9576 and EMD-6999, respectively. All relevant data supporting the findings of this study are available from the authors upon request. We are indebted to staff at beamlines TPS 05A, TLS 13B1, 13C1, and 15A1 at the National Synchrotron Radiation Research Center (NSRRC) in Taiwan, Eiki Yamashita at the Beamline BL44XU, and Taiwan beamline BL12B2 at SPring-8 in Japan for technical assistance under the proposal numbers 2015A6600, 2015A4000, 2015B6600, 2015B4004, 2015B4010, 2016A6600, 2016A6659, 2016A4012, 2016B6600, 2016B4000, 2017A4000, 2017A6600, and 2017B6659, partly supported by the International Collaborative Research Program of the Institute for Protein Research, Osaka University (ICR-16-05). We thank Tomitake Tsukihara for valuable discussions. We are also grateful for Shang-Rung Wu for the assistance of the negative-staining EM measurement at National Cheng Kung University (NCKU). Portions of this research were carried out at the NSRRC-NCKU Protein Crystallography Laboratory. This work was supported in part by National Science Council (NSC) and Ministry of Science and Technology (MOST) grants 101-2628-B-213-001-MY4, 102-2627-M-213-001-MY3, 105-2311-B-213-001-MY3 and NSRRC grants to C.-J. Chen. Author Contributions: C.J.C. initiated the project and designed the research; N.C.C. designed, expressed, purified and crystallized proteins and viral particles; N.C.C., M.Y., H.H.G., P.C., C.C.L, S.K.C, P.J.L., Y.C.H., and C.J.C. performed X-ray data collection and analyses; N.C.C., M.Y., and C.J.C. determined and refined crystal structures; N.M. and K.I. provided cryo-EM facilities, carried out cryo-EM experiment and EM maps; N.C.C., N.M., M.Y., and C.J.C. built and refined cryo-EM structures; N.C.C., M.Y., N.M., H.H.G., and C.J.C. analyzed structures; A.N. provided the collaborative BL44XU beamtime and discussion; N.C.C., M.Y., and C.J.C. wrote the manuscript and prepared the figures; N.C.C., M.Y., C.J.C., and S.I.C. edited and revised the manuscript. The authors declare no competing interests.
Funding AgencyGrant Number
Osaka UniversityICR-16-05
Ministry of Science and Technology (Taipei)101-2628-B-213-001-MY4
Ministry of Science and Technology (Taipei)102-2627-M-213-001-MY3
Ministry of Science and Technology (Taipei)105-2311-B-213-001-MY3
National Synchrotron Radiation Research CenterUNSPECIFIED
Subject Keywords:Electron microscopy; Virus structures; X-ray crystallography
PubMed Central ID:PMC6382870
Record Number:CaltechAUTHORS:20190301-081007422
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:93376
Deposited By: Tony Diaz
Deposited On:01 Mar 2019 16:19
Last Modified:03 Oct 2019 20:53

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