4WIZ | pdb_00004wiz

Crystal structure of Grouper nervous necrosis virus-like particle at 3.6A

• PDB DOI: https://doi.org/10.2210/pdb4WIZ/pdb

• Classification: VIRUS
• Organism(s): Epinephelus coioides nervous necrosis virus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-09-28 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: 3.60 Å
• R-Value Free: 
  0.297 (Depositor), 0.294 (DCC) 
• R-Value Work: 
  0.255 (Depositor), 0.255 (DCC) 
• R-Value Observed: 
  0.257 (Depositor) 

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 180-mer - A180 

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

Macromolecule Content 

• Total Structure Weight: 3,344.02 kDa 
• Atom Count: 203,250 
• Modeled Residue Count: 26,310 
• Deposited Residue Count: 30,420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coat protein	A [auth BA], AA [auth CI], AB [auth AR], AC [auth Ba], B [auth AA], BA [auth BJ], BB [auth CR], BC [auth Aa], C [auth CA], CA [auth AJ], CB [auth BS], CC [auth Ca], D [auth BB], DA [auth CJ], DB [auth AS], DC [auth Bb], E [auth AB], EA [auth BK], EB [auth CS], EC [auth Ab], F [auth CB], FA [auth AK], FB [auth BT], FC [auth Cb], G [auth BC], GA [auth CK], GB [auth AT], GC [auth Bc], H [auth AC], HA [auth BL], HB [auth CT], HC [auth Ac], I [auth CC], IA [auth AL], IB [auth BU], IC [auth Cc], J [auth BD], JA [auth CL], JB [auth AU], JC [auth Bd], K [auth AD], KA [auth BM], KB [auth CU], KC [auth Ad], L [auth CD], LA [auth AM], LB [auth BV], LC [auth Cd], M [auth BE], MA [auth CM], MB [auth AV], N [auth AE], NA [auth BN], NB [auth CV], O [auth CE], OA [auth AN], OB [auth BW], P [auth BF], PA [auth CN], PB [auth AW], Q [auth AF], QA [auth BO], QB [auth CW], R [auth CF], RA [auth AO], RB [auth BX], S [auth BG], SA [auth CO], SB [auth AX], T [auth AG], TA [auth BP], TB [auth CX], U [auth CG], UA [auth AP], UB [auth BY], V [auth BH], VA [auth CP], VB [auth AY], W [auth AH], WA [auth BQ], WB [auth CY], X [auth CH], XA [auth AQ], XB [auth BZ], Y [auth BI], YA [auth CQ], YB [auth AZ], Z [auth AI], ZA [auth BR], ZB [auth CZ]	338	Epinephelus coioides nervous necrosis virus	Mutation(s): 1
UniProt
Find proteins for Q8JNX5 (Epinephelus coioides nervous necrosis virus) Explore Q8JNX5  Go to UniProtKB:  Q8JNX5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	AD [auth AE], AE [auth BN], AF [auth BW], BD [auth BF], BE [auth AN], BF [auth BW], CD [auth BF], CE [auth BO], CF [auth AW], DD [auth AF], DE [auth BO], DF [auth BX], ED [auth BG], EE [auth AO], EF [auth BX], FD [auth BG], FE [auth BP], FF [auth AX], GD [auth AG], GE [auth BP], GF [auth BY], HD [auth BH], HE [auth AP], HF [auth BY], ID [auth BH], IE [auth BQ], IF [auth AY], JD [auth AH], JE [auth BQ], JF [auth BZ], KD [auth BI], KE [auth AQ], KF [auth BZ], LD [auth BI], LE [auth BR], LF [auth AZ], MC [auth BA], MD [auth AI], ME [auth BR], MF [auth Ba], NC [auth BA], ND [auth BJ], NE [auth AR], NF [auth Ba], OC [auth AA], OD [auth BJ], OE [auth BS], OF [auth Aa], PC [auth BB], PD [auth AJ], PE [auth BS], PF [auth Bb], QC [auth BB], QD [auth BK], QE [auth AS], QF [auth Bb], RC [auth AB], RD [auth BK], RE [auth BT], RF [auth Ab], SC [auth BC], SD [auth AK], SE [auth BT], SF [auth Bc], TC [auth BC], TD [auth BL], TE [auth AT], TF [auth Bc], UC [auth AC], UD [auth BL], UE [auth BU], UF [auth Ac], VC [auth BD], VD [auth AL], VE [auth BU], VF [auth Bd], WC [auth BD], WD [auth BM], WE [auth AU], WF [auth Bd], XC [auth AD], XD [auth BM], XE [auth BV], XF [auth Ad], YC [auth BE], YD [auth AM], YE [auth BV], ZC [auth BE], ZD [auth BN], ZE [auth AV]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free:  0.297 (Depositor), 0.294 (DCC) 
• R-Value Work:  0.255 (Depositor), 0.255 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 477.355	α = 90
b = 422.735	β = 134.03
c = 337.893	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data processing
HKL-2000	data scaling
REFMAC	refinement

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: 2015-10-21
  Changes: Derived calculations
• Version 1.2: 2015-11-04
  Changes: Database references
• Version 1.3: 2020-02-05
  Changes: Data collection
• Version 1.4: 2024-03-20
  Changes: Data collection, Database references, Derived calculations