4RFT

T=1 subviral particle of Grouper nervous necrosis virus capsid protein deletion mutant (delta 1-34 & 218-338)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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

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.

(2015) Plos Pathog. 11: e1005203-e1005203

  • DOI: 10.1371/journal.ppat.1005203
  • Primary Citation of Related Structures:  

  • 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 avera ...

    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.


    Organizational Affiliation

    Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan; Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan.,Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan.,Institute for Protein Research, Osaka University, Suita, Osaka, Japan.,Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan; Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan; Department of Physics, National Tsing Hua University, Hsinchu, Taiwan; Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan.,Institute for Protein Research, Osaka University, Suita, Osaka, Japan; Picobiology Institute, Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo, Japan.,Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan.,Institute of Chemistry, Academia Sinica, Taipei, Taiwan; Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United State of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coat protein
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x
183Epinephelus coioides nervous necrosis virusMutation(s): 0 
Find proteins for Q8JNX5 (Epinephelus coioides nervous necrosis virus)
Go to UniProtKB:  Q8JNX5
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.238 
  • Space Group: P 42
Unit Cell:
Length (Å)Angle (°)
a = 288.947α = 90.00
b = 288.947β = 90.00
c = 175.124γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2015-11-04
    Type: Database references