4RFT | pdb_00004rft

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

• PDB DOI: https://doi.org/10.2210/pdb4RFT/pdb

• Classification: VIRUS
• Organism(s): Epinephelus coioides nervous necrosis virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-09-27 Released: 2015-10-07 
• Deposition Author(s): Chen, N.C., Chen, C.J., Yoshimura, M., Guan, H.H., Chen, T.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.288 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

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

• PubMed: 26491970 
• DOI: https://doi.org/10.1371/journal.ppat.1005203
• Primary Citation 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 3.6 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.

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

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 60-mer - A60 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 1,189.04 kDa 
• Atom Count: 75,180 
• Modeled Residue Count: 9,780 
• Deposited Residue Count: 10,980 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coat protein	A, AA [auth 0], AB [auth q], B, BA [auth 1], BB [auth r], C, CA [auth 2], CB [auth s], D, DA [auth 3], DB [auth t], E, EA [auth 4], EB [auth u], F, FA [auth 5], FB [auth v], G, GA [auth 6], GB [auth w], H, HA [auth 7], HB [auth x], I, IA [auth 8], J, JA [auth 9], K, KA [auth a], L, LA [auth b], M, MA [auth c], N, NA [auth d], O, OA [auth e], P, PA [auth f], Q, QA [auth g], R, RA [auth h], S, SA [auth i], T, TA [auth j], U, UA [auth k], V, VA [auth l], W, WA [auth m], X, XA [auth n], Y, YA [auth o], Z, ZA [auth p]	183	Epinephelus coioides nervous necrosis virus	Mutation(s): 0
UniProt
Find proteins for Q8JNX5 (Epinephelus coioides nervous necrosis virus) Explore Q8JNX5  Go to UniProtKB:  Q8JNX5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.288 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 4₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 288.947	α = 90
b = 288.947	β = 90
c = 175.124	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-07 
Deposition Author(s): Chen, N.C., Chen, C.J., Yoshimura, M., Guan, H.H., Chen, T.Y.

Revision History  

• Version 1.0: 2015-10-07
  Type: Initial release
  
• Version 1.1: 2015-11-04
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description