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- PDB-4wiz: Crystal structure of Grouper nervous necrosis virus-like particle... -

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Basic information

Entry
Database: PDB / ID: 4wiz
TitleCrystal structure of Grouper nervous necrosis virus-like particle at 3.6A
ComponentsCoat protein
KeywordsVIRUS / Betanodavirus
Function / homologyNodavirus capsid / nodavirus capsid protein / Viral coat protein subunit / viral capsid / metal ion binding / Capsid protein alpha
Function and homology information
Biological speciesEpinephelus coioides nervous necrosis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 3.6 Å
AuthorsChen, N.C. / Chen, C.J. / Yoshimura, M. / Guan, H.H. / Chen, T.Y.
CitationJournal: Plos Pathog. / Year: 2015
Title: Crystal Structures of a Piscine Betanodavirus: Mechanisms of Capsid Assembly and Viral Infection
Authors: 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.
History
DepositionSep 28, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Derived calculations
Revision 1.2Nov 4, 2015Group: Database references
Revision 1.3Feb 5, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
BA: Coat protein
AA: Coat protein
CA: Coat protein
BB: Coat protein
AB: Coat protein
CB: Coat protein
BC: Coat protein
AC: Coat protein
CC: Coat protein
BD: Coat protein
AD: Coat protein
CD: Coat protein
BE: Coat protein
AE: Coat protein
CE: Coat protein
BF: Coat protein
AF: Coat protein
CF: Coat protein
BG: Coat protein
AG: Coat protein
CG: Coat protein
BH: Coat protein
AH: Coat protein
CH: Coat protein
BI: Coat protein
AI: Coat protein
CI: Coat protein
BJ: Coat protein
AJ: Coat protein
CJ: Coat protein
BK: Coat protein
AK: Coat protein
CK: Coat protein
BL: Coat protein
AL: Coat protein
CL: Coat protein
BM: Coat protein
AM: Coat protein
CM: Coat protein
BN: Coat protein
AN: Coat protein
CN: Coat protein
BO: Coat protein
AO: Coat protein
CO: Coat protein
BP: Coat protein
AP: Coat protein
CP: Coat protein
BQ: Coat protein
AQ: Coat protein
CQ: Coat protein
BR: Coat protein
AR: Coat protein
CR: Coat protein
BS: Coat protein
AS: Coat protein
CS: Coat protein
BT: Coat protein
AT: Coat protein
CT: Coat protein
BU: Coat protein
AU: Coat protein
CU: Coat protein
BV: Coat protein
AV: Coat protein
CV: Coat protein
BW: Coat protein
AW: Coat protein
CW: Coat protein
BX: Coat protein
AX: Coat protein
CX: Coat protein
BY: Coat protein
AY: Coat protein
CY: Coat protein
BZ: Coat protein
AZ: Coat protein
CZ: Coat protein
Ba: Coat protein
Aa: Coat protein
Ca: Coat protein
Bb: Coat protein
Ab: Coat protein
Cb: Coat protein
Bc: Coat protein
Ac: Coat protein
Cc: Coat protein
Bd: Coat protein
Ad: Coat protein
Cd: Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,344,021180
Polymers3,340,41490
Non-polymers3,60790
Water00
1
BA: Coat protein
AA: Coat protein
CA: Coat protein
BB: Coat protein
AB: Coat protein
CB: Coat protein
BC: Coat protein
AC: Coat protein
CC: Coat protein
BD: Coat protein
AD: Coat protein
CD: Coat protein
BE: Coat protein
AE: Coat protein
CE: Coat protein
BF: Coat protein
AF: Coat protein
CF: Coat protein
BG: Coat protein
AG: Coat protein
CG: Coat protein
BH: Coat protein
AH: Coat protein
CH: Coat protein
BI: Coat protein
AI: Coat protein
CI: Coat protein
BJ: Coat protein
AJ: Coat protein
CJ: Coat protein
BK: Coat protein
AK: Coat protein
CK: Coat protein
BL: Coat protein
AL: Coat protein
CL: Coat protein
BM: Coat protein
AM: Coat protein
CM: Coat protein
BN: Coat protein
AN: Coat protein
CN: Coat protein
BO: Coat protein
AO: Coat protein
CO: Coat protein
BP: Coat protein
AP: Coat protein
CP: Coat protein
BQ: Coat protein
AQ: Coat protein
CQ: Coat protein
BR: Coat protein
AR: Coat protein
CR: Coat protein
BS: Coat protein
AS: Coat protein
CS: Coat protein
BT: Coat protein
AT: Coat protein
CT: Coat protein
BU: Coat protein
AU: Coat protein
CU: Coat protein
BV: Coat protein
AV: Coat protein
CV: Coat protein
BW: Coat protein
AW: Coat protein
CW: Coat protein
BX: Coat protein
AX: Coat protein
CX: Coat protein
BY: Coat protein
AY: Coat protein
CY: Coat protein
BZ: Coat protein
AZ: Coat protein
CZ: Coat protein
Ba: Coat protein
Aa: Coat protein
Ca: Coat protein
Bb: Coat protein
Ab: Coat protein
Cb: Coat protein
Bc: Coat protein
Ac: Coat protein
Cc: Coat protein
Bd: Coat protein
Ad: Coat protein
Cd: Coat protein
hetero molecules

BA: Coat protein
AA: Coat protein
CA: Coat protein
BB: Coat protein
AB: Coat protein
CB: Coat protein
BC: Coat protein
AC: Coat protein
CC: Coat protein
BD: Coat protein
AD: Coat protein
CD: Coat protein
BE: Coat protein
AE: Coat protein
CE: Coat protein
BF: Coat protein
AF: Coat protein
CF: Coat protein
BG: Coat protein
AG: Coat protein
CG: Coat protein
BH: Coat protein
AH: Coat protein
CH: Coat protein
BI: Coat protein
AI: Coat protein
CI: Coat protein
BJ: Coat protein
AJ: Coat protein
CJ: Coat protein
BK: Coat protein
AK: Coat protein
CK: Coat protein
BL: Coat protein
AL: Coat protein
CL: Coat protein
BM: Coat protein
AM: Coat protein
CM: Coat protein
BN: Coat protein
AN: Coat protein
CN: Coat protein
BO: Coat protein
AO: Coat protein
CO: Coat protein
BP: Coat protein
AP: Coat protein
CP: Coat protein
BQ: Coat protein
AQ: Coat protein
CQ: Coat protein
BR: Coat protein
AR: Coat protein
CR: Coat protein
BS: Coat protein
AS: Coat protein
CS: Coat protein
BT: Coat protein
AT: Coat protein
CT: Coat protein
BU: Coat protein
AU: Coat protein
CU: Coat protein
BV: Coat protein
AV: Coat protein
CV: Coat protein
BW: Coat protein
AW: Coat protein
CW: Coat protein
BX: Coat protein
AX: Coat protein
CX: Coat protein
BY: Coat protein
AY: Coat protein
CY: Coat protein
BZ: Coat protein
AZ: Coat protein
CZ: Coat protein
Ba: Coat protein
Aa: Coat protein
Ca: Coat protein
Bb: Coat protein
Ab: Coat protein
Cb: Coat protein
Bc: Coat protein
Ac: Coat protein
Cc: Coat protein
Bd: Coat protein
Ad: Coat protein
Cd: Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,688,043360
Polymers6,680,829180
Non-polymers7,214180
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
4
BA: Coat protein
AA: Coat protein
CA: Coat protein
BB: Coat protein
AB: Coat protein
CB: Coat protein
BC: Coat protein
AC: Coat protein
CC: Coat protein
BD: Coat protein
AD: Coat protein
CD: Coat protein
BE: Coat protein
AE: Coat protein
CE: Coat protein
BF: Coat protein
AF: Coat protein
CF: Coat protein
BG: Coat protein
AG: Coat protein
CG: Coat protein
BH: Coat protein
AH: Coat protein
CH: Coat protein
BI: Coat protein
AI: Coat protein
CI: Coat protein
BJ: Coat protein
AJ: Coat protein
CJ: Coat protein
BK: Coat protein
AK: Coat protein
CK: Coat protein
BL: Coat protein
AL: Coat protein
CL: Coat protein
BM: Coat protein
AM: Coat protein
CM: Coat protein
BN: Coat protein
AN: Coat protein
CN: Coat protein
BO: Coat protein
AO: Coat protein
CO: Coat protein
BP: Coat protein
AP: Coat protein
CP: Coat protein
BQ: Coat protein
AQ: Coat protein
CQ: Coat protein
BR: Coat protein
AR: Coat protein
CR: Coat protein
BS: Coat protein
AS: Coat protein
CS: Coat protein
BT: Coat protein
AT: Coat protein
CT: Coat protein
BU: Coat protein
AU: Coat protein
CU: Coat protein
BV: Coat protein
AV: Coat protein
CV: Coat protein
BW: Coat protein
AW: Coat protein
CW: Coat protein
BX: Coat protein
AX: Coat protein
CX: Coat protein
BY: Coat protein
AY: Coat protein
CY: Coat protein
BZ: Coat protein
AZ: Coat protein
CZ: Coat protein
Ba: Coat protein
Aa: Coat protein
Ca: Coat protein
Bb: Coat protein
Ab: Coat protein
Cb: Coat protein
Bc: Coat protein
Ac: Coat protein
Cc: Coat protein
Bd: Coat protein
Ad: Coat protein
Cd: Coat protein
hetero molecules


  • crystal asymmetric unit, crystal frame
  • 3.34 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)3,344,021180
Polymers3,340,41490
Non-polymers3,60790
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
Unit cell
Length a, b, c (Å)477.355, 422.735, 337.893
Angle α, β, γ (deg.)90.000, 134.030, 90.000
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Components on special symmetry positions
IDModelComponents
11BI-318-

GLU

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Components

#1: Protein ...
Coat protein


Mass: 37115.715 Da / Num. of mol.: 90 / Mutation: T214N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epinephelus coioides nervous necrosis virus
Production host: Escherichia coli (E. coli) / References: UniProt: Q8JNX5
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 90 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.67 Å3/Da / Density % sol: 66.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.2 M Sodium formate, 20% (w/v) PEG 3350, pH7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.6→266 Å / Num. obs: 549703 / % possible obs: 98.9 % / Redundancy: 3.9 % / Net I/σ(I): 7.2

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Processing

Software
NameVersionClassification
HKL-2000data processing
HKL-2000data scaling
REFMAC5.8.0049refinement
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 3.6→263.91 Å / Cor.coef. Fo:Fc: 0.848 / Cor.coef. Fo:Fc free: 0.809 / Occupancy max: 1 / Occupancy min: 1 / SU B: 41.4 / SU ML: 0.596 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.68 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2968 27556 5 %RANDOM
Rwork0.2546 522147 --
obs0.2567 549703 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 449.48 Å2 / Biso mean: 103.7458 Å2 / Biso min: 19.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å20 Å2
2---0.02 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 3.6→263.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms203160 0 90 0 203250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02208260
X-RAY DIFFRACTIONr_bond_other_d0.0040.02192810
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.949284970
X-RAY DIFFRACTIONr_angle_other_deg1.0623442650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.384526220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7923.4859210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.7271531260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.138151590
X-RAY DIFFRACTIONr_chiral_restr0.10.232280
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021238650
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0248540
X-RAY DIFFRACTIONr_mcbond_it14.14810.06105150
X-RAY DIFFRACTIONr_mcbond_other14.14810.06105149
X-RAY DIFFRACTIONr_mcangle_it22.37115.061131280
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 1905 -
Rwork0.36 36166 -
all-38071 -
obs--92.93 %

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