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- PDB-3ide: Structure of IPNV subviral particle -

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Basic information

Entry
Database: PDB / ID: 3ide
TitleStructure of IPNV subviral particle
ComponentsCapsid protein VP2
KeywordsVIRUS LIKE PARTICLE / Jelly roll / beta sandwich / icosahedral particle / Virion
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / viral capsid / host cell cytoplasm / structural molecule activity / proteolysis / metal ion binding
Similarity search - Function
icosahedral virus / Birnavirus VP3, domain 2 / Birnavirus VP3, domain 1 / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protease domain / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protein / Birnavirus VP4 protease domain profile. ...icosahedral virus / Birnavirus VP3, domain 2 / Birnavirus VP3, domain 1 / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protease domain / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protein / Birnavirus VP4 protease domain profile. / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Structural polyprotein
Similarity search - Component
Biological speciesInfectious pancreatic necrosis virus -
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.35 Å
AuthorsCoulibaly, F. / Chevalier, C. / Delmas, B. / Rey, F.A.
CitationJournal: J.Virol. / Year: 2010
Title: Crystal structure of an aquabirnavirus particle: insights into antigenic diversity and virulence determinism
Authors: Coulibaly, F. / Chevalier, C. / Delmas, B. / Rey, F.A.
History
DepositionJul 21, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein VP2
B: Capsid protein VP2
C: Capsid protein VP2
D: Capsid protein VP2
E: Capsid protein VP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,14111
Polymers242,8575
Non-polymers2836
Water18010
1
A: Capsid protein VP2
B: Capsid protein VP2
C: Capsid protein VP2
D: Capsid protein VP2
E: Capsid protein VP2
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)2,917,687132
Polymers2,914,28960
Non-polymers3,39872
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
Unit cell
Length a, b, c (Å)303.431, 303.431, 303.431
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11C-443-

CO

21C-444-

CL

31E-443-

CO

41E-444-

CL

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALATHRTHRchain A and (resseq 6:109 or resseq 118:428 )AA6 - 1096 - 109
12ASNASNASNASNchain A and (resseq 6:109 or resseq 118:428 )AA118 - 428118 - 428
21ALAALATHRTHRchain B and (resseq 6:109 or resseq 118:428 )BB6 - 1096 - 109
22ASNASNASNASNchain B and (resseq 6:109 or resseq 118:428 )BB118 - 428118 - 428
31ALAALATHRTHRchain C and (resseq 6:109 or resseq 118:428 )CC6 - 1096 - 109
32ASNASNASNASNchain C and (resseq 6:109 or resseq 118:428 )CC118 - 428118 - 428
41ALAALATHRTHRchain D and (resseq 6:109 or resseq 118:428 )DD6 - 1096 - 109
42ASNASNASNASNchain D and (resseq 6:109 or resseq 118:428 )DD118 - 428118 - 428
51ALAALATHRTHRchain E and (resseq 6:109 or resseq 118:428 )EE6 - 1096 - 109
52ASNASNASNASNchain E and (resseq 6:109 or resseq 118:428 )EE118 - 428118 - 428

NCS oper:
IDCodeMatrixVector
1given(0.810781, 0.303649, -0.500432), (0.308983, 0.504104, 0.806479), (0.497156, -0.808503, 0.314896)58.607101, -94.007599, 150.990997
2given(0.501223, 0.806866, -0.312639), (0.812262, -0.314144, 0.491471), (0.298337, -0.500282, -0.812843)0.361525, 1.83655, 305.247986
3given(0.491694, 0.814407, 0.308185), (0.813667, -0.303659, -0.495719), (-0.310134, 0.494502, -0.811963)-93.073196, 149.927994, 246.520996
4given(0.805853, 0.312112, 0.503177), (0.307898, 0.504986, -0.806342), (-0.505767, 0.80472, 0.310846)-94.399002, 150.972, 58.7901
DetailsThe entry contains the asymmetric unit of the T=1 icosahedral particle.

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Components

#1: Protein
Capsid protein VP2 / / PP


Mass: 48571.488 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious pancreatic necrosis virus - / Strain: Sp / Gene: VP2 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q703G9
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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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: 4.79 Å3/Da / Density % sol: 74.34 % / Mosaicity: 0.405 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: 1M 1,6-hexanediol, 10mM CoCl2, 100mM sodium acetate pH 4.6, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.95 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 28, 2003
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 14.62 / Number: 557145 / Rmerge(I) obs: 0.112 / Χ2: 1.01 / D res high: 3.75 Å / D res low: 28 Å / Num. obs: 46708 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
8.022899.410.0560.995
6.398.0210010.0680.999
5.596.3910010.0951.015
5.085.5910010.1050.999
4.725.0810010.1121
4.444.7210010.1311.017
4.224.4410010.1781.009
4.044.2210010.2581.014
3.884.0410010.3831.013
3.753.8810010.4631.038
ReflectionResolution: 3.35→30 Å / Num. all: 66352 / Num. obs: 66153 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 85.3 Å2 / Rmerge(I) obs: 0.08 / Χ2: 1.03 / Net I/σ(I): 16.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
3.35-3.473.20.3793.364911.11298.3
3.47-3.610.24165510.99499.5
3.61-3.770.20366071.03899.8
3.77-3.970.17265491.06199.8
3.97-4.220.11266111.01999.9
4.22-4.540.08365961.01899.9
4.54-50.06866321.0599.9
5-5.720.06466571.03399.9
5.72-7.190.05666571.0199.9
7.19-300.05468020.99699.7

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: SIRAS / Resolution: 3.35→29.754 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 1992 3.04 %12 RESOLUTION SHELL
Rwork0.2171 ---
all0.218 66372 --
obs0.218 65456 98.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.876 Å2 / ksol: 0.265 e/Å3
Displacement parametersBiso max: 248.21 Å2 / Biso mean: 99.951 Å2 / Biso min: 20.18 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.35→29.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16056 0 6 10 16072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00516356
X-RAY DIFFRACTIONf_angle_d0.91822267
X-RAY DIFFRACTIONf_chiral_restr0.0652599
X-RAY DIFFRACTIONf_plane_restr0.0032897
X-RAY DIFFRACTIONf_dihedral_angle_d18.016011
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3208X-RAY DIFFRACTIONPOSITIONAL0.014
12B3208X-RAY DIFFRACTIONPOSITIONAL0.014
13C3208X-RAY DIFFRACTIONPOSITIONAL0.016
14D3208X-RAY DIFFRACTIONPOSITIONAL0.013
15E3208X-RAY DIFFRACTIONPOSITIONAL0.021
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.35-3.4340.3081660.3344446461298
3.434-3.5270.372830.314540462398
3.527-3.630.2721660.3094527469399
3.63-3.7470.3161660.2844497466399
3.747-3.8810.3121660.2824493465999
3.881-4.0360.3830.2744562464598
4.036-4.2190.2581660.2354447461398
4.219-4.4410.2191660.2094442460898
4.441-4.7180.207830.184537462098
4.718-5.0810.1591660.1684439460598
5.081-5.5890.2021660.1754572473899
5.589-6.3910.201830.1794622470599
6.391-8.0260.1961660.16946334799100
8.026-29.7550.1791660.17747074873100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.31180.0144-0.49072.11030.61230.9636-0.24140.1584-0.0790.64440.06610.12140.4726-0.32030.17280.6869-0.14610.0610.5377-0.06940.610466.8874135.3274127.5307
20.48210.45490.66541.8119-0.15251.47840.0348-0.2208-0.1524-0.4370.11410.28190.4655-0.3935-0.14510.6663-0.1963-0.02660.5540.02890.683765.9286137.0218173.384
30.3772-0.01470.54540.7363-0.12780.1988-0.0350.14740.0231-0.3063-0.02840.14050.15550.0570.04890.6739-0.10180.02090.61170.1330.575388.7542100.6508189.2645
41.0237-0.5098-0.19720.0364-0.18861.79250.00170.1073-0.42980.00610.07820.2259-0.1868-0.5722-0.08520.5734-0.06870.00730.72540.06840.7673103.617275.9217153.1406
50.60450.1384-0.04120.7601-0.2390.5274-0.0157-0.2083-0.00540.22140.06380.1306-0.097-0.0609-0.04220.5384-0.0614-0.01550.5468-0.05670.482890.389697.7562115.138
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA6 - 428
2X-RAY DIFFRACTION2chain BB6 - 428
3X-RAY DIFFRACTION3chain CC6 - 428
4X-RAY DIFFRACTION4chain DD6 - 428
5X-RAY DIFFRACTION5chain EE6 - 428

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