4RFU

Crystal structure of truncated P-domain from Grouper nervous necrosis virus capsid protein at 1.2A

Summary for 4RFU

• Entry DOI: 10.2210/pdb4rfu/pdb
• Related: 4RFT 4WIZ
• Descriptor: Coat protein, CALCIUM ION, GLYCEROL, ... (5 entities in total)
• Functional Keywords: protrusion domain, viral protein
• Biological source: Epinephelus coioides nervous necrosis virus
• Total number of polymer chains: 3
• Total formula weight: 42051.36

Authors

Chen, N.C.,Chen, C.J.,Yoshimura, M.,Guan, H.H.,Chen, T.Y. (deposition date: 2014-09-27, release date: 2015-10-07, Last modification date: 2023-11-08)

Primary citation

Chen, N.C.,Yoshimura, M.,Guan, H.H.,Wang, T.Y.,Misumi, Y.,Lin, C.C.,Chuankhayan, P.,Nakagawa, A.,Chan, S.I.,Tsukihara, T.,Chen, T.Y.,Chen, C.J.
Crystal Structures of a Piscine Betanodavirus: Mechanisms of Capsid Assembly and Viral Infection
Plos Pathog., 11:e1005203-e1005203, 2015

PubMed 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.

PubMed: 26491970
DOI: 10.1371/journal.ppat.1005203

Experimental method

X-RAY DIFFRACTION (1.2 Å)