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- PDB-5cdc: Crystal Structure of Israel acute Paralysis Virus -

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Basic information

Entry
Database: PDB / ID: 5cdc
TitleCrystal Structure of Israel acute Paralysis Virus
Components
  • VP1, Structural polyprotein
  • VP2, Structural polyprotein
  • VP3, Structural polyprotein
  • VP4
KeywordsVIRUS / Virion / capsid / honeybee virus / pathogen
Function / homology
Function and homology information


structural molecule activity
Similarity search - Function
Capsid protein VP4, dicistrovirus / Cricket paralysis virus, VP4 / Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesIsraeli acute paralysis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4 Å
AuthorsMullapudi, E. / Plevka, P.
CitationJournal: J.Virol. / Year: 2016
Title: Virion Structure of Iflavirus Slow Bee Paralysis Virus at 2.6-Angstrom Resolution.
Authors: Kalynych, S. / Pridal, A. / Palkova, L. / Levdansky, Y. / de Miranda, J.R. / Plevka, P.
History
DepositionJul 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_wavelength_list
Revision 1.4May 30, 2018Group: Data collection / Source and taxonomy / Category: entity_src_nat
Item: _entity_src_nat.common_name / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific
Revision 1.5Jan 10, 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 / 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_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

Downloads & links

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Assembly

Deposited unit
A: VP1, Structural polyprotein
B: VP2, Structural polyprotein
C: VP3, Structural polyprotein
D: VP4


Theoretical massNumber of molelcules
Total (without water)87,6614
Polymers87,6614
Non-polymers00
Water00
1
A: VP1, Structural polyprotein
B: VP2, Structural polyprotein
C: VP3, Structural polyprotein
D: VP4
x 60


Theoretical massNumber of molelcules
Total (without water)5,259,664240
Polymers5,259,664240
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: VP1, Structural polyprotein
B: VP2, Structural polyprotein
C: VP3, Structural polyprotein
D: VP4
x 5


  • icosahedral pentamer
  • 438 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)438,30520
Polymers438,30520
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1, Structural polyprotein
B: VP2, Structural polyprotein
C: VP3, Structural polyprotein
D: VP4
x 6


  • icosahedral 23 hexamer
  • 526 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)525,96624
Polymers525,96624
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
Unit cell
Length a, b, c (Å)343.149, 383.261, 329.911
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.31806453, -0.76845058, 0.5552645), (0.84959281, 0.49094665, 0.19277821), (-0.42074578, 0.41043281, 0.80902281)101.79343, 81.77116, -63.01766
3generate(-0.78533024, -0.39378634, 0.47769105), (0.60621946, -0.33271897, 0.72235452), (-0.12551648, 0.85687246, 0.50001521)36.34174, 196.25098, -123.26797
4generate(-0.78533023, 0.60621947, -0.12551647), (-0.39378635, -0.33271897, 0.85687246), (0.47769105, 0.72235452, 0.50001521)-105.90305, 185.23223, -97.48705
5generate(0.31806454, 0.84959281, -0.42074578), (-0.76845058, 0.49094665, 0.41043281), (0.5552645, 0.19277822, 0.8090228)-128.36348, 63.94245, -21.30325
6generate(-1, 3.05E-6), (-1, -1.994E-5), (3.04E-6, -1.994E-5, 1)-0.00362, 383.2948, 0.00382
7generate(-0.31806581, 0.76845183, -0.55526203), (-0.84958442, -0.49095484, -0.19279435), (-0.42076176, 0.41042068, 0.80902065)-101.79724, 301.52489, -63.01516
8generate(0.78532985, 0.39378896, -0.47768953), (-0.60621696, 0.33270188, -0.72236449), (-0.12553095, 0.85687789, 0.50000226)-36.34573, 187.04628, -123.26795
9generate(0.78533169, -0.60621726, 0.125518), (0.39377682, 0.33270456, -0.85688243), (0.47769651, 0.722363, 0.49999774)105.89914, 198.06452, -97.48724
10generate(-0.31806284, -0.84959222, 0.42074825), (0.76843951, -0.4909505, -0.41044895), (0.55528079, 0.19277101, 0.80901334)128.3598, 319.35277, -21.3011
11generate(-0.9052551, 0.42486845, 4.09E-6), (0.42486845, 0.9052551, 1.835E-5), (4.09E-6, 1.835E-5, -1)-81.42813, 18.15675, 163.79716
12generate(0.07303392, 0.90423323, -0.42074733), (0.90422609, 0.11794908, 0.41044267), (0.42076267, -0.41042695, -0.809017)-138.83542, 135.42817, 226.81674
13generate(0.96848721, 0.21511881, -0.12552457), (0.21511892, -0.46848721, 0.85688014), (0.12552439, -0.85688017, -0.5)-30.94633, 211.25214, 287.06888
14generate(0.54361876, -0.6901421, 0.47768454), (-0.69013037, -0.04361876, 0.72236935), (-0.47770149, -0.72235815, -0.5)93.14008, 140.84251, 261.28718
15generate(-0.61441768, -0.56050969, 0.55526552), (-0.56049803, 0.80540068, 0.19279964), (-0.5552773, -0.19276573, -0.80901699)61.94061, 21.50299, 185.10107
16generate(0.9052551, -0.42486845, -7.14E-6), (-0.42486845, -0.9052551, 1.59E-6), (-7.13E-6, 1.59E-6, -1)81.42501, 365.13478, 163.80038
17generate(-0.07303264, -0.90423448, 0.42074486), (-0.90423448, -0.1179409, -0.41042654), (0.42074486, -0.41042655, -0.80902646)138.8325, 247.8621, 226.81744
18generate(-0.96848683, -0.21512142, 0.12552305), (-0.21512142, 0.4685043, -0.85687017), (0.12552304, -0.85687018, -0.50001747)30.94359, 172.03693, 287.06839
19generate(-0.54362021, 0.6901399, -0.47768607), (0.6901399, 0.04363316, -0.72235938), (-0.47768607, -0.72235937, -0.50001295)-93.1429, 242.44708, 261.28847
20generate(0.61441598, 0.5605091, -0.55526799), (0.56050911, -0.80539684, -0.1927835), (-0.55526799, -0.1927835, -0.80901915)-61.94367, 361.78811, 185.10465
21generate(0.21243604, -0.04738069, 0.97602561), (0.95262505, -0.21244179, -0.2176557), (0.2176613, 0.97602436, 5.75E-6)-70.85781, 250.18801, -105.1515
22generate(-0.38334458, 0.21408494, 0.89845121), (0.21408494, -0.92567589, 0.31191629), (0.8984512, 0.3119163, 0.30902048)-114.61444, 343.50352, -3.18472
23generate(-0.31806284, 0.7684395, 0.55528079), (-0.84959222, -0.4909505, 0.19277102), (0.42074824, -0.41044894, 0.80901334)-192.74871, 269.94613, 94.30372
24generate(0.31806412, 0.84958383, 0.42076422), (-0.76844075, 0.49095868, -0.41043681), (-0.55527833, -0.19278715, 0.80901119)-197.28172, 131.16965, 52.58811
25generate(0.64593046, 0.34537922, 0.68079882), (0.34539078, 0.66308653, -0.66409447), (-0.68079296, 0.66410048, 0.309017)-121.949, 118.95846, -70.68199
26generate(-0.21243308, 0.04736123, 0.9760272), (-0.95262571, 0.21244613, -0.21764856), (-0.2176613, -0.97602436, -1.305E-5)-89.01562, 168.7559, 268.95278
27generate(-0.43798899, 0.58708974, 0.68080194), (-0.03092903, 0.74701538, -0.6640869), (-0.89844813, -0.3119193, -0.30902639)-168.27407, 102.87253, 166.98646
28generate(0.07303392, 0.90422609, 0.42076267), (0.90423323, 0.11794908, -0.41042695), (-0.42074732, 0.41044268, -0.80901699)-207.75401, 202.65767, 69.49846
29generate(0.61441937, 0.56049862, 0.55527483), (0.56049862, -0.80540453, 0.19278186), (0.55527484, 0.19278187, -0.80901484)-152.89549, 330.21165, 111.21388
30generate(0.43799106, 0.03092701, 0.89844718), (-0.58710332, -0.74700214, 0.31192546), (0.6807889, -0.66410189, -0.30902291)-79.51113, 309.2592, 234.48343
31generate(-0.21243538, 0.04738367, -0.97602561), (-0.95262939, 0.21242232, 0.2176557), (0.21764296, 0.97602846, 1.305E-5)70.85387, 133.10889, -105.15288
32generate(0.38334733, -0.21408399, -0.89845026), (-0.21410286, 0.92566967, -0.31192246), (0.89844577, 0.31193541, 0.30901699)114.61081, 39.79135, -3.1881
33generate(0.31806413, -0.76844076, -0.55527832), (0.84958383, 0.49095868, -0.19278715), (0.42076421, -0.41043682, 0.80901118)192.74538, 113.34679, 94.30157
34generate(-0.31806581, -0.84958442, -0.42076175), (0.76845183, -0.49095484, 0.41042068), (-0.55526204, -0.19279435, 0.80902065)197.27826, 252.1241, 52.58872
35generate(-0.64593254, -0.3453772, -0.68079787), (-0.3453772, -0.66309977, 0.66408831), (-0.68079788, 0.66408831, 0.30903231)121.94517, 264.33775, -70.68091
36generate(0.21243241, -0.04736421, -0.9760272), (0.95263005, -0.21242666, 0.21764856), (-0.21764296, -0.97602846, -5.75E-6)89.01282, 214.53354, 268.95296
37generate(0.43798625, -0.5870907, -0.68080288), (0.03094695, -0.74700916, 0.66409306), (-0.89844884, -0.31193241, -0.30901108)168.27097, 280.41894, 166.98772
38generate(-0.0730352, -0.90422484, -0.42076514), (-0.90422484, -0.11795727, 0.41044308), (-0.42076513, 0.41044308, -0.80900753)207.7506, 180.63574, 69.49761
39generate(-0.61441767, -0.56049803, -0.5552773), (-0.56050969, 0.80540068, -0.19276573), (0.55526553, 0.19279963, -0.809017)152.89221, 53.08093, 111.21065
40generate(-0.43798898, -0.03092904, -0.89844813), (0.58708974, 0.74701538, -0.3119193), (0.68080194, -0.6640869, -0.3090264)79.50823, 74.03092, 234.48084
41generate(0.21243605, 0.95262505, 0.2176613), (-0.0473807, -0.21244179, 0.97602436), (0.97602561, -0.2176557, 5.74E-6)-200.3952, 152.42352, 123.61448
42generate(0.78533169, 0.39377682, 0.47769651), (-0.60621727, 0.33270456, 0.722363), (0.125518, -0.85688243, 0.49999774)-114.58985, 68.72209, 205.16916
43generate(0.38334731, -0.21410286, 0.89844577), (-0.21408399, 0.92566968, 0.31193541), (-0.89845027, -0.31192246, 0.309017)-32.55197, -11.30282, 116.3691
44generate(-0.43798833, -0.03094493, 0.8984479), (0.58710427, 0.74699592, 0.31193857), (-0.68078984, 0.66410805, -0.30900759)-67.65512, 22.94048, -20.06702
45generate(-0.5436173, 0.69013258, 0.47769997), (0.69013257, 0.04360435, 0.72236811), (0.47769997, 0.72236812, -0.49998705)-171.38794, 124.12893, -15.58913
46generate(-0.21243539, -0.95262939, 0.21764295), (0.04738367, 0.21242233, 0.97602845), (-0.97602561, 0.2176557, 1.306E-5)164.74109, 70.99959, 40.18466
47generate(-0.96848759, -0.21511631, -0.12552591), (-0.21511631, 0.46847012, 0.85689014), (-0.12552591, 0.85689014, -0.49998253)51.50361, 31.68593, -41.3712
48generate(-0.43798832, 0.58710427, -0.68078983), (-0.03094493, 0.74699592, 0.66410805), (0.89844791, 0.31193857, -0.3090076)-56.76203, -5.90336, 47.42772
49generate(0.64593047, 0.34539077, -0.68079296), (0.34537922, 0.66308653, 0.66410048), (0.68079882, -0.66409447, 0.30901699)-10.43638, 10.17884, 183.86433
50generate(0.78532985, -0.60621696, -0.12553096), (0.39378895, 0.33270188, 0.85687789), (-0.47768953, -0.72236449, 0.50000226)126.46008, 57.70748, 179.38787
51generate(0.21243241, 0.95263005, -0.21764295), (-0.0473642, -0.21242667, -0.97602845), (-0.97602721, 0.21764856, -5.74E-6)-164.74459, 312.29441, 40.18756
52generate(0.96848721, 0.21511892, 0.12552438), (0.21511881, -0.46848721, -0.85688017), (-0.12552456, 0.85688015, -0.5)-51.50735, 351.6097, -41.36785
53generate(0.43799106, -0.58710332, 0.68078889), (0.03092701, -0.74700214, -0.66410189), (0.89844719, 0.31192546, -0.30902291)56.75856, 389.19721, 47.43149
54generate(-0.64592839, -0.3453928, 0.6807939), (-0.34539279, -0.66307329, -0.66410664), (0.6807939, -0.66410664, 0.30900168)10.43333, 373.11229, 183.86791
55generate(-0.78533131, 0.60621476, 0.12553248), (-0.39377943, -0.33268747, -0.85688786), (-0.47769499, -0.72237297, 0.49998479)-126.46315, 325.58375, 179.39092
56generate(-0.21243307, -0.95262571, -0.2176613), (0.04736123, 0.21244613, -0.97602436), (0.97602721, -0.21764856, -1.306E-5)200.39196, 230.86882, 123.61466
57generate(-0.7853313, -0.39377943, -0.47769498), (0.60621476, -0.33268747, -0.72237297), (0.12553247, -0.85688786, 0.49998479)114.58686, 314.56861, 205.17126
58generate(-0.38335006, 0.21410191, -0.89844482), (0.21410191, -0.92566345, -0.31194157), (-0.89844483, -0.31194157, 0.30901351)32.54871, 394.5953, 116.37305
59generate(0.43798625, 0.03094695, -0.89844885), (-0.58709069, -0.74700916, -0.3119324), (-0.68080288, 0.66409306, -0.30901108)67.65144, 360.35472, -20.06386
60generate(0.54361876, -0.69013037, -0.47770149), (-0.6901421, -0.04361876, -0.72235814), (0.47768455, 0.72236934, -0.5)171.38427, 259.16619, -15.5883

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Components

#1: Protein VP1, Structural polyprotein


Mass: 23370.121 Da / Num. of mol.: 1 / Fragment: residues 706-908 / Source method: isolated from a natural source / Source: (natural) Israeli acute paralysis virus / References: UniProt: D1FK67
#2: Protein VP2, Structural polyprotein


Mass: 33266.758 Da / Num. of mol.: 1 / Fragment: residues 401-699 / Source method: isolated from a natural source / Source: (natural) Israeli acute paralysis virus / References: UniProt: D1FK67
#3: Protein VP3, Structural polyprotein


Mass: 27176.455 Da / Num. of mol.: 1 / Fragment: residues 28-270 / Source method: isolated from a natural source / Source: (natural) Israeli acute paralysis virus / References: UniProt: D1FK67
#4: Protein/peptide VP4


Mass: 3847.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Due to the poor resolution of the structure the register of the amino acids for chain D remain unknown.
Source: (natural) Israeli acute paralysis virus

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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

Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.5
Details: 0.1M Cadmium chloride, 0.1M Naacetate pH 4.5, 15% (v/v) PEG 400
PH range: 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 4→70 Å / Num. all: 668296 / Num. obs: 262425 / % possible obs: 72.7 % / Redundancy: 2.5 % / Net I/σ(I): 1.09

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
CNSrefinement
PHASERphasing
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B35

1b35


Resolution: 4→70 Å / Cross valid method: NONE / σ(F): 0
Num. reflection% reflection
Rfree0 0 %
Rwork250379 -
obs250379 68.8 %
Solvent computationBsol: 73.2556 Å2
Displacement parametersBiso max: 400 Å2 / Biso mean: 130.4322 Å2 / Biso min: 10 Å2
Baniso -1Baniso -2Baniso -3
1--3.198 Å20 Å2-0 Å2
2---5.988 Å2-0 Å2
3---9.186 Å2
Refinement stepCycle: final / Resolution: 4→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6120 0 0 0 6120
Num. residues----791
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param

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