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- PDB-1wcd: Crystal structure of IBDV T1 virus-like particle reveals a missin... -

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Basic information

Entry
Database: PDB / ID: 1wcd
TitleCrystal structure of IBDV T1 virus-like particle reveals a missing link in icosahedral viruses evolution
ComponentsMAJOR STRUCTURAL PROTEIN VP2
KeywordsVIRUS / NON-ENVELOPED ICOSAHEDRAL VIRUSES / DOUBLE-STRANDED RNA VIRUS PROTEIN / BIRNAVIRUS / TRANSCRIPTASE MACHINERY / HYDROLASE / MEMBRANE TRANSLOCATION ACTIVITY / EVOLUTION / ICOSAHEDRAL VIRUS
Function / homology
Function and homology information


T=13 icosahedral viral capsid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / 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 BURSAL DISEASE VIRUS (Gumboro virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCoulibaly, F. / Chevalier, C. / Gutsche, I. / Pous, J. / Bressanelli, S. / Navaza, J. / Delmas, B. / Rey, F.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2005
Title: The Birnavirus Crystal Structure Reveals Structural Relationships Among Icosahedral Viruses.
Authors: Coulibaly, F. / Chevalier, C. / Gutsche, I. / Pous, J. / Navaza, J. / Bressanelli, S. / Delmas, B. / Rey, F.A.
History
DepositionNov 12, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
J: MAJOR STRUCTURAL PROTEIN VP2


Theoretical massNumber of molelcules
Total (without water)47,1921
Polymers47,1921
Non-polymers00
Water66737
1
J: MAJOR STRUCTURAL PROTEIN VP2
x 60


Theoretical massNumber of molelcules
Total (without water)2,831,52760
Polymers2,831,52760
Non-polymers00
Water1,08160
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
J: MAJOR STRUCTURAL PROTEIN VP2
x 5


  • icosahedral pentamer
  • 236 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)235,9615
Polymers235,9615
Non-polymers00
Water905
TypeNameSymmetry operationNumber
point symmetry operation5
4
J: MAJOR STRUCTURAL PROTEIN VP2
x 6


  • icosahedral 23 hexamer
  • 283 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)283,1536
Polymers283,1536
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
J: MAJOR STRUCTURAL PROTEIN VP2
x 20


  • crystal asymmetric unit, crystal frame
  • 944 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)943,84220
Polymers943,84220
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation20
Unit cell
Length a, b, c (Å)258.929, 258.929, 347.186
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.494157, -0.869198, -0.017407), (0.642324, 0.378521, -0.666439), (0.585857, 0.318145, 0.745356)131.44862, 150.71294, -25.47275
3generate(-0.324314, -0.764068, 0.557692), (0.170104, -0.627054, -0.760177), (0.930529, -0.15167, 0.333333)65.84886, 309.16962, 80.49963
4generate(-0.324314, 0.170104, 0.930529), (-0.764068, -0.627054, -0.15167), (0.557692, -0.760177, 0.333333)-106.14265, 256.38829, 171.4669
5generate(0.494157, 0.642324, 0.585857), (-0.869198, 0.378521, 0.318145), (-0.017407, -0.666439, 0.745356)-146.83948, 65.31096, 121.7154
6generate(0.998637, -0.052202), (-0.052202, -0.998637), (-1)7.80388, 298.7815, 173.47825
7generate(0.459952, -0.887773, 0.017407), (-0.667245, -0.33263, 0.666439), (-0.585857, -0.318145, -0.745356)131.20569, 141.41212, 198.951
8generate(-0.332751, -0.730293, 0.596615), (-0.152942, 0.666085, 0.730027), (-0.930529, 0.15167, -0.333333)57.42355, -13.40404, 92.97862
9generate(-0.283985, 0.202606, 0.937178), (0.779956, 0.617319, 0.102887), (-0.557692, 0.760177, -0.333333)-111.57814, 48.2837, 2.01134
10generate(0.538858, 0.621689, 0.56845), (0.842217, -0.411536, -0.348294), (0.017407, 0.666439, -0.745356)-142.24478, 241.22498, 51.76285
11generate(-0.033469, -0.924592, -0.379486), (-0.347242, 0.366803, -0.863064), (0.937178, 0.102887, -0.333333)171.136, 169.51976, 100.27128
12generate(-0.832751, -0.441617, 0.333915), (-0.441617, 0.166085, -0.881697), (0.333915, -0.881697, -0.333333)37.0551, 201.14185, 247.45942
13generate(-0.499546, 0.662898, 0.557692), (-0.628096, 0.166212, -0.760177), (-0.596615, -0.730027, 0.333333)-147.47212, 190.58221, 166.95979
14generate(0.505669, 0.862552, -0.017407), (-0.648971, 0.367009, -0.666439), (-0.56845, 0.348294, 0.745356)-127.43532, 152.43392, -29.97986
15generate(0.79372, -0.118571, -0.596615), (-0.475393, 0.49098, -0.730027), (0.379486, 0.863064, 0.333333)69.47532, 139.41661, -71.19563
16generate(-0.015297, -0.942479, -0.333915), (0.348515, -0.318037, 0.881697), (-0.937178, -0.102887, 0.333333)169.85719, 120.55916, 73.20697
17generate(-0.808562, -0.449685, 0.379486), (0.484487, -0.142805, 0.863064), (-0.333915, 0.881697, 0.333333)34.30837, 95.97954, -73.98117
18generate(-0.466076, 0.653318, 0.596615), (0.653318, -0.20059, 0.730027), (0.596615, 0.730027, -0.333333)-149.41602, 116.15755, 6.51845
19generate(0.538858, 0.842217, 0.017407), (0.621689, -0.411536, 0.666439), (0.56845, -0.348294, -0.745356)-127.41511, 153.20786, 203.4581
20generate(0.817455, -0.14404, -0.557692), (0.433311, -0.484121, 0.760177), (-0.379486, -0.863064, -0.333333)69.90659, 155.9282, 244.67388

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Components

#1: Protein MAJOR STRUCTURAL PROTEIN VP2 / IBDV VP2 SUBVIRAL PARTICLE


Mass: 47192.113 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFECTIOUS BURSAL DISEASE VIRUS (Gumboro virus)
Strain: CT / Description: VACCINE STRAIN (MERIAL) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P15480
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE MATURE VP2 PROTEIN REPRESENTS RESIDUES 1-441 OF THE IBDV POLYPROTEIN. THIS PROTEIN AS WELL AS ...THE MATURE VP2 PROTEIN REPRESENTS RESIDUES 1-441 OF THE IBDV POLYPROTEIN. THIS PROTEIN AS WELL AS VP3 AND VP4 ARE GENERATED BY PROTEOLYTIC PROCESSING OF THE VIRAL POLYPROTEIN

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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: 2.7 Å3/Da / Density % sol: 54 %
Description: MOLECULAR REPLACEMENT STARTING MODEL IS A TRACE OF IPNV VP2. THIS STRUCTURE HAS BEEN SOLVED BY SIR AT 3.4A AND THE MODEL WILL BE DEPOSITED IN THE PDB UPON COMPLETION OF THE REFINEMENT.
Crystal growpH: 5
Details: 100MM SODIUM ACETATE PH 5.0, 30% PEG 400, NACL 100MM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 23, 2002
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 255310 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 64.203 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11
Reflection shellResolution: 3→3.05 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.6 / % possible all: 91

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→40 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TWIN_LSQ
Details: TWINNING OPERATOR K,H,-L TWINNING FRACTION 0.17. ENTRY CONTAINS ZERO OCCUPANCY ATOMS.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 7361 2.8 %SHELLS
Rwork0.219 ---
obs0.219 251175 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.4436 Å2 / ksol: 0.276645 e/Å3
Displacement parametersBiso mean: 56.025 Å2
Baniso -1Baniso -2Baniso -3
1--4.14 Å22.23 Å20 Å2
2---4.14 Å20 Å2
3---8.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3169 0 0 37 3206
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008394
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.53984
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.70022
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8979
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.14 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.35 907
Rwork0.3095 29281
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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