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- PDB-1wce: Crystal structure of the T13 IBDV viral particle reveals a missin... -

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Basic information

Entry
Database: PDB / ID: 1wce
TitleCrystal structure of the T13 IBDV viral 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
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. / Viral coat protein subunit
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesINFECTIOUS BURSAL DISEASE VIRUS (Gumboro virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D, E, F, G, H, I, J, K, L, M
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 6, 2005Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAJOR STRUCTURAL PROTEIN VP2
B: MAJOR STRUCTURAL PROTEIN VP2
C: MAJOR STRUCTURAL PROTEIN VP2
D: MAJOR STRUCTURAL PROTEIN VP2
E: MAJOR STRUCTURAL PROTEIN VP2
F: MAJOR STRUCTURAL PROTEIN VP2
G: MAJOR STRUCTURAL PROTEIN VP2
H: MAJOR STRUCTURAL PROTEIN VP2
I: MAJOR STRUCTURAL PROTEIN VP2
J: MAJOR STRUCTURAL PROTEIN VP2
K: MAJOR STRUCTURAL PROTEIN VP2
L: MAJOR STRUCTURAL PROTEIN VP2
M: MAJOR STRUCTURAL PROTEIN VP2


Theoretical massNumber of molelcules
Total (without water)613,86213
Polymers613,86213
Non-polymers00
Water00
1
A: MAJOR STRUCTURAL PROTEIN VP2
B: MAJOR STRUCTURAL PROTEIN VP2
C: MAJOR STRUCTURAL PROTEIN VP2
D: MAJOR STRUCTURAL PROTEIN VP2
E: MAJOR STRUCTURAL PROTEIN VP2
F: MAJOR STRUCTURAL PROTEIN VP2
G: MAJOR STRUCTURAL PROTEIN VP2
H: MAJOR STRUCTURAL PROTEIN VP2
I: MAJOR STRUCTURAL PROTEIN VP2
J: MAJOR STRUCTURAL PROTEIN VP2
K: MAJOR STRUCTURAL PROTEIN VP2
L: MAJOR STRUCTURAL PROTEIN VP2
M: MAJOR STRUCTURAL PROTEIN VP2
x 60


Theoretical massNumber of molelcules
Total (without water)36,831,728780
Polymers36,831,728780
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: MAJOR STRUCTURAL PROTEIN VP2
B: MAJOR STRUCTURAL PROTEIN VP2
C: MAJOR STRUCTURAL PROTEIN VP2
D: MAJOR STRUCTURAL PROTEIN VP2
E: MAJOR STRUCTURAL PROTEIN VP2
F: MAJOR STRUCTURAL PROTEIN VP2
G: MAJOR STRUCTURAL PROTEIN VP2
H: MAJOR STRUCTURAL PROTEIN VP2
I: MAJOR STRUCTURAL PROTEIN VP2
J: MAJOR STRUCTURAL PROTEIN VP2
K: MAJOR STRUCTURAL PROTEIN VP2
L: MAJOR STRUCTURAL PROTEIN VP2
M: MAJOR STRUCTURAL PROTEIN VP2
x 5


  • icosahedral pentamer
  • 3.07 MDa, 65 polymers
Theoretical massNumber of molelcules
Total (without water)3,069,31165
Polymers3,069,31165
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: MAJOR STRUCTURAL PROTEIN VP2
B: MAJOR STRUCTURAL PROTEIN VP2
C: MAJOR STRUCTURAL PROTEIN VP2
D: MAJOR STRUCTURAL PROTEIN VP2
E: MAJOR STRUCTURAL PROTEIN VP2
F: MAJOR STRUCTURAL PROTEIN VP2
G: MAJOR STRUCTURAL PROTEIN VP2
H: MAJOR STRUCTURAL PROTEIN VP2
I: MAJOR STRUCTURAL PROTEIN VP2
J: MAJOR STRUCTURAL PROTEIN VP2
K: MAJOR STRUCTURAL PROTEIN VP2
L: MAJOR STRUCTURAL PROTEIN VP2
M: MAJOR STRUCTURAL PROTEIN VP2
x 6


  • icosahedral 23 hexamer
  • 3.68 MDa, 78 polymers
Theoretical massNumber of molelcules
Total (without water)3,683,17378
Polymers3,683,17378
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: MAJOR STRUCTURAL PROTEIN VP2
B: MAJOR STRUCTURAL PROTEIN VP2
C: MAJOR STRUCTURAL PROTEIN VP2
D: MAJOR STRUCTURAL PROTEIN VP2
E: MAJOR STRUCTURAL PROTEIN VP2
F: MAJOR STRUCTURAL PROTEIN VP2
G: MAJOR STRUCTURAL PROTEIN VP2
H: MAJOR STRUCTURAL PROTEIN VP2
I: MAJOR STRUCTURAL PROTEIN VP2
J: MAJOR STRUCTURAL PROTEIN VP2
K: MAJOR STRUCTURAL PROTEIN VP2
L: MAJOR STRUCTURAL PROTEIN VP2
M: MAJOR STRUCTURAL PROTEIN VP2
x 60


  • crystal asymmetric unit, crystal frame
  • 36.8 MDa, 780 polymers
Theoretical massNumber of molelcules
Total (without water)36,831,728780
Polymers36,831,728780
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)854.010, 692.230, 792.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.309055, -0.806547, -0.503951), (0.811939, 0.499682, -0.301782), (0.495217, -0.31591, 0.809296)526.37492, 59.61583, 41.39834
3generate(-0.808917, -0.493082, -0.320193), (0.507198, -0.309848, -0.804204), (0.297327, -0.812936, 0.500732)620.10806, 504.29582, 316.73855
4generate(-0.808917, 0.507198, 0.297327), (-0.493082, -0.309848, -0.812936), (-0.320193, -0.804204, 0.500732)151.66341, 719.50733, 445.50982
5generate(0.309055, 0.811939, 0.495217), (-0.806547, 0.499682, -0.31591), (-0.503951, -0.301782, 0.809296)-231.58445, 407.83538, 249.75463
6generate(-0.999998, 1.0E-6, 0.002074), (1.0E-6, -1, 0.000874), (0.002074, 0.000874, 0.999997)426.43601, 692.06127, -0.74445
7generate(-0.308027, 0.805891, 0.505628), (-0.811506, -0.499959, 0.302489), (0.496566, -0.317145, 0.807986)-99.85188, 632.48211, 41.79737
8generate(0.809532, 0.491395, 0.32123), (-0.506938, 0.309138, 0.804641), (0.296092, -0.814227, 0.499364)-193.01347, 188.04293, 317.71976
9generate(0.808251, -0.508864, -0.296289), (0.492801, 0.309146, 0.813373), (-0.3223, -0.803421, 0.500637)275.69739, -27.05642, 445.70734
10generate(-0.3101, -0.812563, -0.493538), (0.806107, -0.499945, 0.316617), (-0.504013, -0.299661, 0.810045)658.53822, 284.44404, 248.88564
11generate(-0.9995, 0.031606, -1.4E-5), (0.031606, 0.9995, -0.000906), (-1.4E-5, -0.000906, -1)415.80392, -6.39311, 396.19268
12generate(-0.283245, 0.821942, 0.494149), (0.820852, 0.474227, -0.318293), (-0.495957, 0.315469, -0.809015)-108.42437, 69.79221, 354.73279
13generate(0.824539, 0.483054, 0.294607), (0.481108, -0.324541, -0.814376), (-0.297775, 0.813223, -0.499998)-188.0599, 516.96289, 78.98837
14generate(0.792933, -0.516726, -0.32288), (-0.518112, -0.292934, -0.803585), (0.320651, 0.804477, -0.499999)286.95093, 717.14426, -49.97116
15generate(-0.334386, -0.795736, -0.504966), (-0.795919, 0.525368, -0.300833), (0.504677, 0.301318, -0.809017)660.15929, 393.69246, 146.07188
16generate(0.999498, -0.031607, -0.002059), (-0.031607, -0.9995, 3.3E-5), (-0.002059, 3.3E-5, -0.999998)11.45453, 698.80089, 396.30386
17generate(0.282217, -0.821286, -0.495826), (-0.821286, -0.47395, 0.317587), (-0.495826, 0.317587, -0.808267)535.59579, 622.57891, 353.82359
18generate(-0.825155, -0.481367, -0.295644), (-0.481367, 0.325252, 0.813939), (-0.295644, 0.813939, -0.500097)614.65976, 175.16741, 78.30541
19generate(-0.792267, 0.518393, 0.321842), (0.518393, 0.293636, 0.803148), (0.321842, 0.803148, -0.501369)139.38273, -25.12611, -49.49391
20generate(0.335431, 0.796359, 0.503287), (0.796359, -0.525106, 0.300126), (0.503287, 0.300126, -0.810325)-233.41861, 298.49717, 147.03994
21generate(0.01475, -0.001723, -0.99989), (0.999759, -0.016234, 0.014776), (-0.016257, -0.999867, 0.001483)408.78824, 135.43901, 547.18521
22generate(-0.492003, 0.303117, -0.816121), (0.303117, -0.819132, -0.486972), (-0.816121, -0.486972, 0.311136)375.05582, 661.33103, 479.08135
23generate(-0.3101, 0.806107, -0.504013), (-0.812563, -0.499945, -0.299661), (-0.493538, 0.316617, 0.810045)100.36225, 751.89134, 33.34523
24generate(0.309075, 0.812131, -0.49489), (-0.805449, 0.500222, 0.317851), (0.505692, 0.300369, 0.808736)-35.6753, 281.96867, -174.03099
25generate(0.509844, 0.312864, -0.801358), (0.314627, 0.799173, 0.512185), (0.800668, -0.513263, 0.309018)154.94244, -99.01982, 143.53958
26generate(-0.016823, 0.00085, -0.999858), (-0.999726, 0.016247, 0.016835), (0.016259, 0.999868, 0.000576)414.62998, 550.52667, -151.7176
27generate(-0.499656, 0.329859, -0.80096), (-0.287442, 0.809127, 0.512534), (0.817142, 0.48632, -0.30947)364.43271, 25.96138, -83.5273
28generate(-0.283245, 0.820852, -0.495957), (0.821942, 0.474227, 0.315469), (0.494149, -0.318293, -0.809015)87.9325, -55.88586, 362.77651
29generate(0.333337, 0.795294, -0.506353), (0.795294, -0.525632, -0.302024), (-0.506353, -0.302024, -0.807705)-32.75676, 418.09504, 570.41713
30generate(0.497995, 0.288505, -0.817781), (-0.330559, -0.808679, -0.48659), (-0.801706, 0.512644, -0.30735)169.15339, 792.8786, 252.44228
31generate(-0.014783, -0.00035, 0.999891), (-0.999773, 0.01536, -0.014776), (-0.015353, -0.999882, -0.000577)18.78343, 557.10074, 547.40538
32generate(0.49031, -0.304127, 0.816763), (-0.303831, 0.818707, 0.487243), (-0.816874, -0.487058, 0.309017)52.37503, 31.14939, 479.6912
33generate(0.309075, -0.805449, 0.505692), (0.812131, 0.500222, 0.300369), (-0.49489, 0.317851, 0.808736)326.14381, -59.80056, 33.46571
34generate(-0.308027, -0.811506, 0.496566), (0.805891, -0.499959, -0.317145), (0.505628, 0.302489, 0.807986)461.75062, 409.94063, -174.60263
35generate(-0.508182, -0.313927, 0.801998), (-0.313927, -0.79962, -0.511915), (0.801998, -0.511915, 0.307803)271.79146, 791.2066, 143.02955
36generate(0.016856, 0.001224, 0.999857), (0.99974, -0.015374, -0.016835), (0.015351, 0.999881, -0.001482)11.49282, 141.40263, -151.1209
37generate(0.50135, -0.328849, 0.800317), (0.288155, -0.808701, -0.512805), (0.815853, 0.48771, -0.310682)61.8309, 666.02725, -83.49316
38generate(0.28427, -0.82151, 0.494279), (-0.82151, -0.474504, -0.316176), (0.494279, -0.316176, -0.809766)339.25591, 748.26414, 362.16465
39generate(-0.334386, -0.795919, 0.504677), (-0.795736, 0.525368, 0.301318), (-0.504966, -0.300833, -0.809017)460.37591, 274.46471, 569.96858
40generate(-0.499656, -0.287442, 0.817142), (0.329859, 0.809127, 0.48632), (-0.80096, 0.512534, -0.30947)257.80717, -100.59633, 252.74067
41generate(0.01475, 0.999759, -0.016257), (-0.001723, -0.016234, -0.999867), (-0.99989, 0.014776, 0.001483)-132.54035, 550.0154, 405.93019
42generate(0.808251, 0.492801, -0.3223), (-0.508864, 0.309146, -0.803421), (-0.296289, 0.813373, 0.500637)-65.84781, 506.74771, -119.44438
43generate(0.49031, -0.303831, -0.816874), (-0.304127, 0.818707, -0.487058), (0.816763, 0.487243, 0.309017)375.63133, 224.06394, -206.18807
44generate(-0.499689, -0.289218, -0.816495), (0.329548, 0.808253, -0.487981), (0.801067, -0.512913, -0.308564)581.78792, 92.62345, 265.57594
45generate(-0.793601, 0.516444, -0.321686), (0.516444, 0.292231, -0.804914), (-0.321686, -0.804914, -0.49863)267.72054, 294.07253, 643.88583
46generate(-0.014783, -0.999773, -0.015353), (-0.00035, 0.01536, -0.999882), (0.999891, -0.014776, -0.000577)565.65624, 538.79029, -10.23388
47generate(-0.823926, -0.482796, 0.296739), (-0.482796, 0.32383, -0.81366), (0.296739, -0.81366, -0.499904)497.63702, 498.12825, 515.17872
48generate(-0.499689, 0.329548, 0.801067), (-0.289218, 0.808253, -0.512913), (-0.816495, -0.487981, -0.308564)47.44506, 229.618, 602.17224
49generate(0.509844, 0.314627, 0.800668), (0.312864, 0.799173, -0.513263), (-0.801358, 0.512185, 0.309018)-162.76964, 104.33157, 130.52458
50generate(0.809532, -0.506938, 0.296092), (0.491395, 0.309138, -0.814227), (0.32123, 0.804641, 0.499364)157.50248, 295.41055, -247.96322
51generate(0.016856, 0.99974, 0.015351), (0.001224, -0.015374, 0.999881), (0.999857, -0.016835, -0.001482)-139.23975, 153.26276, -9.33463
52generate(0.824539, 0.481108, -0.297775), (0.483054, -0.324541, 0.813223), (0.294607, -0.814376, -0.499998)-70.1312, 194.38375, 515.90008
53generate(0.497995, -0.330559, -0.801706), (0.288505, -0.808679, 0.512644), (-0.817781, -0.48659, -0.30735)380.23994, 462.9695, 601.72526
54generate(-0.511504, -0.313564, -0.800026), (-0.313564, -0.798724, 0.513534), (-0.800026, 0.513534, 0.310229)589.47605, 587.84363, 129.53343
55generate(-0.808864, 0.508606, -0.295057), (-0.491113, -0.308435, 0.814663), (0.323337, 0.803858, 0.499265)268.41995, 396.43433, -248.12235
56generate(-0.016823, -0.999726, 0.016259), (0.00085, 0.016247, 0.999868), (-0.999858, 0.016835, 0.000576)559.81832, 142.40061, 405.39041
57generate(-0.808864, -0.491113, 0.323337), (0.508606, -0.308435, 0.803858), (-0.295057, 0.814663, 0.499265)492.03646, 185.20933, -119.88234
58generate(-0.488616, 0.304841, 0.817512), (0.304841, -0.818281, 0.487327), (0.817512, 0.487327, 0.306897)50.37813, 467.81761, -205.95733
59generate(0.50135, 0.288155, 0.815853), (-0.328849, -0.808701, 0.48771), (0.800317, -0.512805, -0.310682)-154.79987, 599.67041, 266.11815
60generate(0.792933, -0.518112, 0.320651), (-0.516726, -0.292934, 0.804477), (-0.32288, -0.803585, -0.499999)160.05148, 398.55164, 643.95183

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Components

#1: Protein
MAJOR STRUCTURAL PROTEIN VP2 / IBDV VP2 SUBVIRAL PARTICLE / Coordinate model: Cα atoms only


Mass: 47220.164 Da / Num. of mol.: 13 / Fragment: RESIDUES 1-441 / Source method: isolated from a natural source / Details: VACCINE STRAIN (MERIAL)
Source: (natural) INFECTIOUS BURSAL DISEASE VIRUS (Gumboro virus)
Strain: CT / References: UniProt: P15480

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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: 3.4 Å3/Da / Density % sol: 64 %
Description: THE DATA WERE PROCESSED IN SPACE GROUP P21. THE 00L, L-ODD REFLECTIONS APPEAR WEAK IN THE REFLECTION FILE. THE AUTHORS SUGGEST THAT THIS IS LIKELY DUE TO THE ICOSAHEDRAL NON- ...Description: THE DATA WERE PROCESSED IN SPACE GROUP P21. THE 00L, L-ODD REFLECTIONS APPEAR WEAK IN THE REFLECTION FILE. THE AUTHORS SUGGEST THAT THIS IS LIKELY DUE TO THE ICOSAHEDRAL NON-CRYSTALLOGRAPHIC SYMMETRY OF THE VIRAL PARTICLE
Crystal growpH: 7.5
Details: 1.6% PEG8000 0.5M KSCN 100 MM HEPES PH7.5 20% GLYCEROL 20% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.72017
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 4, 2004
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72017 Å / Relative weight: 1
ReflectionResolution: 7→50 Å / Num. obs: 1089650 / % possible obs: 75.1 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 5.68
Reflection shellResolution: 7→7.7 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.72 / % possible all: 63.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
UROphasing
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WCD

1wcd


Resolution: 7→50 Å / σ(F): 5.68
Details: THE MODEL WAS BUILT AS DOCKING FROM AN EM MAP. RIGID BODY REFINEMENT FROM T1 PARTICLE (PDB ID 1WCD)
Num. reflection% reflection
obs1089650 75.1 %
Refinement stepCycle: LAST / Resolution: 7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5533 0 0 0 5533
LS refinement shellResolution: 7→50 Å

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