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

• Published in: PLoS pathogens Vol. 11; no. 10; p. e1005203
• Main Authors: Chen, Nai-Chi, Yoshimura, Masato, Guan, Hong-Hsiang, Wang, Ting-Yu, Misumi, Yuko, Lin, Chien-Chih, Chuankhayan, Phimonphan, Nakagawa, Atsushi, Chan, Sunney I, Tsukihara, Tomitake, Chen, Tzong-Yueh, Chen, Chun-Jung
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.10.2015; Public Library of Science (PLoS)
• Subjects: Atoms & subatomic particles; Calcium - metabolism; Capsid Proteins - chemistry; Crystallography, X-Ray; Crystals; Data collection; Fishes; Gangrene; Genomes; Health aspects; Infections; Mortality; NOD-like receptors; Nodaviridae - chemistry; Phylogenetics; Polyethylene glycol; Polyethylene Glycols - pharmacology; Protein Structure, Tertiary; Proteins; RNA polymerase; Structure; Viral infections; Virion - chemistry; Virus Assembly; Viruses; Taiwan
• ISSN: 1553-7374; 1553-7366; 1553-7374
• DOI: 10.1371/journal.ppat.1005203

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.