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: 3.10 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.241 

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:  
    4RFT, 4RFU, 4WIZ

  • 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 ...

    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; Department of Physics, National Tsing Hua University, Hsinchu, Taiwan; Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coat protein183Epinephelus coioides nervous necrosis virusMutation(s): 0 
UniProt
Find proteins for Q8JNX5 (Epinephelus coioides nervous necrosis virus)
Explore Q8JNX5 
Go to UniProtKB:  Q8JNX5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JNX5
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.241 
  • Space Group: P 42
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 288.947α = 90
b = 288.947β = 90
c = 175.124γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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