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Crystal Structures of a Piscine Betanodavirus: Mechanisms of Capsid Assembly and Viral Infection

Chen, Nai-Chi and Yoshimura, Masato and Guan, Hong-Hsiang and Wang, Ting-Yu and Misumi, Yuko and Lin, Chien-Chih and Chuankhayan, Phimonphan and Nakagawa, Atsushi and Chan, Sunney I. and Tsukihara, Tomitake and Chen, Tzong-Yueh and Chen, Chun-Jung (2015) Crystal Structures of a Piscine Betanodavirus: Mechanisms of Capsid Assembly and Viral Infection. PLoS Pathogens, 11 (10). Art. No. e1005203. ISSN 1553-7366. PMCID PMC4619592. https://resolver.caltech.edu/CaltechAUTHORS:20151103-082920090

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[img] Image (TIFF) (S1 Fig. Structural determination of the T = 3 GNNV-LPs by the ab initio method with NCSA) - Supplemental Material
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[img] Image (TIFF) (S2 Fig. EM images of GNNV-LPs of different capsid organization) - Supplemental Material
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[img] Image (TIFF) (S3 Fig. Crystal packing and self-rotation function of the T = 1 N-ARM deletion mutant) - Supplemental Material
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[img] Image (TIFF) (S4 Fig. Structural organization of the S-domain) - Supplemental Material
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[img] Image (TIFF) (S5 Fig. Structural comparison of the P-domains among GNNV, Orsay virus, HEV and Calicivirus) - Supplemental Material
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[img] Image (TIFF) (S6 Fig. Specific arrangement of water molecules in the P-domain and the Ca2+-mediated oligomerization of GNNV CP) - Supplemental Material
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[img] Image (TIFF) (S7 Fig. The Ca2+-binding and ligand-binding pockets of the P-domain) - Supplemental Material
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[img] Image (TIFF) (S8 Fig. Phylogenetic tree and sequence alignment of CPs of the family Nodaviridae) - Supplemental Material
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Abstract

Betanodaviruses cause massive mortality in marine fish species with viral nervous necrosis. The structure of a T = 3 Grouper nervous necrosis virus-like particle (GNNV-LP) is determined by the ab initio method with non-crystallographic symmetry averaging at 3.6 Å resolution. Each capsid protein (CP) shows three major domains: (i) the N-terminal arm, an inter-subunit extension at the inner surface; (ii) the shell domain (S-domain), a jelly-roll structure; and (iii) the protrusion domain (P-domain) formed by three-fold trimeric protrusions. In addition, we have determined structures of the T = 1 subviral particles (SVPs) of (i) the delta-P-domain mutant (residues 35−217) at 3.1 Å resolution; and (ii) the N-ARM deletion mutant (residues 35−338) at 7 Å resolution; and (iii) the structure of the individual P-domain (residues 214−338) at 1.2 Å resolution. The P-domain reveals a novel DxD motif asymmetrically coordinating two Ca2+ ions, and seems to play a prominent role in the calcium-mediated trimerization of the GNNV CPs during the initial capsid assembly process. The flexible N-ARM (N-terminal arginine-rich motif) appears to serve as a molecular switch for T = 1 or T = 3 assembly. Finally, we find that polyethylene glycol, which is incorporated into the P-domain during the crystallization process, enhances GNNV infection. The present structural studies together with the biological assays enhance our understanding of the role of the P-domain of GNNV in the capsid assembly and viral infection by this betanodavirus.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1371/journal.ppat.1005203DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4619592/PubMed CentralArticle
ORCID:
AuthorORCID
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:© 2015 Chen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Received: March 31, 2015; Accepted: September 11, 2015; Published: October 22, 2015. This work was supported in part by Ministry of Science and Technology (MOST) grants 98-2313-B-009-001-MY3, 101-2628-B-213-001-MY4, 102-2627-M-213-001-MY3 and NSRRC grants 1023RSB02, 1023RSB14, 10324RSB02 and 10324RSB14 to C-J Chen. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors have declared that no competing interests exist. We are indebted to the staff at beamlines BL13B1, BL13C1 and BL15A1 at the National Synchrotron Radiation Research Center (NSRRC) in Taiwan and the staff at the Taiwan contracted beamline BL12B2 and Eiki Yamashita at the BL44XU at SPring-8 in Japan for technical assistance under the proposal numbers 2012A4009, 2012A6760, 2012A6600, 2012B4002, 2012B4012, 2012B6600, 2013A4011, 2013A6600, 2013B4000, 2013B6600, 2014A4000, 2014A6600, 2014A6965 and 2014A4004. We thank Ting-Fang Wang for the SUMO expression vector. We thank Christina Ling Chang, Yee-Shin Lin and KC Han-Ching Wang for valuable discussion. Portions of this research were carried out at the NSRRC-NCKU Protein Crystallography Laboratory of the University Center for Bioscience and Biotechnology of National Cheng Kung University (NCKU). Author Contributions: Conceived and designed the experiments: CJC TYC NCC. Performed the experiments: NCC YM HHG TYW CCL PC CJC. Analyzed the data: NCC MY TT TYW TYC CJC. Contributed reagents/materials/analysis tools: AN. Wrote the paper: NCC CJC. Revised the paper: NCC MY SIC AN TYC CJC.
Funders:
Funding AgencyGrant Number
Ministry of Science and Technology (Taipei)98-2313-B-009-001-MY3
Ministry of Science and Technology (Taipei)101-2628-B-213-001-MY4
Ministry of Science and Technology (Taipei)102-2627-M-213-001-MY3
National Synchrotron Radiation Research Center (NSRRC)1023RSB02
National Synchrotron Radiation Research Center (NSRRC)1023RSB14
National Synchrotron Radiation Research Center (NSRRC)10324RSB02
National Synchrotron Radiation Research Center (NSRRC)10324RSB14
Issue or Number:10
PubMed Central ID:PMC4619592
Record Number:CaltechAUTHORS:20151103-082920090
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20151103-082920090
Official Citation:Chen N-C, Yoshimura M, Guan H-H, Wang T-Y, Misumi Y, Lin C-C, et al. (2015) Crystal Structures of a Piscine Betanodavirus: Mechanisms of Capsid Assembly and Viral Infection. PLoS Pathog 11(10): e1005203. doi:10.1371/journal.ppat.1005203
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:61785
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:03 Nov 2015 19:44
Last Modified:09 Mar 2020 13:19

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