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- PDB-2xgk: Virus like particle of L172W mutant of Minute Virus of Mice - the... -

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Basic information

Entry
Database: PDB / ID: 2xgk
TitleVirus like particle of L172W mutant of Minute Virus of Mice - the immunosuppressive strain
ComponentsCOAT PROTEIN VP2
KeywordsVIRUS / VLP / PARVOVIRUS
Function / homology
Function and homology information


permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / microtubule-dependent intracellular transport of viral material towards nucleus / T=1 icosahedral viral capsid / viral penetration into host nucleus / clathrin-dependent endocytosis of virus by host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / metal ion binding
Similarity search - Function
Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Biological speciesMURINE MINUTE VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsPlevka, P. / Hafenstein, S. / Tattersall, P. / Cotmore, S. / Farr, G. / D'Abramo, A. / Rossmann, M.G.
CitationJournal: J.Virol. / Year: 2011
Title: Structure of a Packaging-Defective Mutant of Minute Virus of Mice Indicates that the Genome is Packaged Via a Pore at a 5-Fold Axis.
Authors: Plevka, P. / Hafenstein, S. / Li, L. / D'Abrgamo, A. / Cotmore, S.F. / Rossmann, M.G. / Tattersall, P.
History
DepositionJun 4, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Structure summary
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 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: COAT PROTEIN VP2


Theoretical massNumber of molelcules
Total (without water)64,8191
Polymers64,8191
Non-polymers00
Water0
1
A: COAT PROTEIN VP2
x 60


Theoretical massNumber of molelcules
Total (without water)3,889,11960
Polymers3,889,11960
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: COAT PROTEIN VP2
x 5


  • icosahedral pentamer
  • 324 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)324,0935
Polymers324,0935
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: COAT PROTEIN VP2
x 6


  • icosahedral 23 hexamer
  • 389 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)388,9126
Polymers388,9126
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: COAT PROTEIN VP2
x 60
A: COAT PROTEIN VP2
x 60


  • crystal asymmetric unit, crystal frame
  • 7.78 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)7,778,239120
Polymers7,778,239120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z3
point symmetry operation118
transform to crystal frame1
Unit cell
Length a, b, c (Å)442.900, 411.100, 301.800
Angle α, β, γ (deg.)90.00, 95.88, 90.00
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.959943, -0.141521, 0.241827), (0.141521, -0.5, -0.854384), (0.241827, 0.854384, -0.459943)
3generate(0.959943, 0.141521, 0.241827), (-0.141521, -0.5, 0.854384), (0.241827, -0.854384, -0.459943)
4generate(0.920505, -0.390731), (-1), (-0.390731, -0.920505)
5generate(0.789143, -0.464105, 0.402317), (-0.141521, 0.5, 0.854384), (-0.597683, -0.731168, 0.328891)
6generate(0.789143, 0.464105, 0.402317), (0.141521, 0.5, -0.854384), (-0.597683, 0.731168, 0.328891)
7generate(0.39154, -0.89246, -0.22408), (0.89246, 0.309017, 0.32867), (-0.22408, -0.32867, 0.917477)
8generate(0.195366, 0.199368, 0.960252), (0.979925, -0.199368), (-0.039748, 0.979925, -0.195366)
9generate(0.44797, 0.693092, -0.564754), (0.89246, -0.309017, 0.32867), (0.05328, -0.651254, -0.756987)
10generate(0.44797, 0.89246, 0.05328), (0.693092, -0.309017, -0.651254), (-0.564754, 0.32867, -0.756987)
11generate(0.569212, -0.464105, -0.678678), (0.464105, -0.5, 0.731168), (-0.678678, -0.731168, -0.069212)
12generate(0.316608, -0.428354, 0.846328), (0.55157, 0.809017, 0.203129), (-0.771706, 0.402497, 0.492409)
13generate(-0.592969, -0.55157, -0.58665), (0.55157, -0.809017, 0.203129), (-0.58665, -0.203129, 0.783952)
14generate(-0.789143, -0.141521, 0.597683), (0.464105, 0.5, 0.731168), (-0.402317, 0.854384, -0.328891)
15generate(-0.633025, 0.693092, -0.344823), (0.693092, 0.309017, -0.651254), (-0.344823, -0.651254, -0.675992)
16generate(-0.316608, 0.55157, 0.771706), (0.428354, 0.809017, -0.402497), (-0.846328, 0.203129, -0.492409)
17generate(-0.039248, 0.428354, -0.902758), (0.428354, -0.809017, -0.402497), (-0.902758, -0.402497, -0.151735)
18generate(-0.195366, -0.979925, 0.039748), (0.199368, 0.979925), (-0.960252, 0.199368, 0.195366)
19generate(-0.592969, 0.55157, -0.58665), (-0.55157, -0.809017, -0.203129), (-0.58665, 0.203129, 0.783952)
20generate(-0.633025, -0.693092, -0.344823), (-0.693092, 0.309017, 0.651254), (-0.344823, 0.651254, -0.675992)
21generate(-0.789143, 0.141521, 0.597683), (-0.464105, 0.5, -0.731168), (-0.402317, -0.854384, -0.328891)
22generate(-0.316608, -0.55157, 0.771706), (-0.428354, 0.809017, 0.402497), (-0.846328, -0.203129, -0.492409)
23generate(-0.195366, 0.979925, 0.039748), (-0.199368, -0.979925), (-0.960252, -0.199368, 0.195366)
24generate(-0.039248, -0.428354, -0.902758), (-0.428354, -0.809017, 0.402497), (-0.902758, 0.402497, -0.151735)
25generate(0.39154, 0.89246, -0.22408), (-0.89246, 0.309017, -0.32867), (-0.22408, 0.32867, 0.917477)
26generate(0.44797, -0.693092, -0.564754), (-0.89246, -0.309017, -0.32867), (0.05328, 0.651254, -0.756987)
27generate(0.195366, -0.199368, 0.960252), (-0.979925, 0.199368), (-0.039748, -0.979925, -0.195366)
28generate(0.44797, -0.89246, 0.05328), (-0.693092, -0.309017, 0.651254), (-0.564754, -0.32867, -0.756987)
29generate(0.316608, 0.428354, 0.846328), (-0.55157, 0.809017, -0.203129), (-0.771706, -0.402497, 0.492409)
30generate(0.569212, 0.464105, -0.678678), (-0.464105, -0.5, -0.731168), (-0.678678, 0.731168, -0.069212)
31generate(0.745476, 0.666533), (1), (-0.666533, 0.745476)205.98199, 150.08099
32generate(0.8768, 0.463974, -0.126291), (0.141521, -0.5, -0.854384), (-0.459557, 0.731251, -0.504062)205.98199, 150.08099
33generate(0.8768, -0.463974, -0.126291), (-0.141521, -0.5, 0.854384), (-0.459557, -0.731251, -0.504062)205.98199, 150.08099
34generate(0.425779, -0.904827), (-1), (-0.904827, -0.425779)205.98199, 150.08099
35generate(0.189912, -0.833327, 0.519134), (-0.141521, 0.5, 0.854384), (-0.971548, -0.235727, -0.022977)205.98199, 150.08099
36generate(0.189912, 0.833327, 0.519134), (0.141521, 0.5, -0.854384), (-0.971548, 0.235727, -0.022977)205.98199, 150.08099
37generate(0.142527, -0.884377, 0.444482), (0.89246, 0.309017, 0.32867), (-0.428021, 0.349838, 0.833314)205.98199, 150.08099
38generate(0.119147, 0.801776, 0.585628), (0.979925, -0.199368), (-0.159848, 0.597625, -0.78568)205.98199, 150.08099
39generate(0.369464, 0.082601, -0.925567), (0.89246, -0.309017, 0.32867), (-0.258867, -0.947463, -0.187889)205.98199, 150.08099
40generate(-0.042476, 0.884377, -0.464837), (0.693092, -0.309017, -0.651254), (-0.719597, -0.349838, -0.599828)205.98199, 150.08099
41generate(-0.028027, -0.833327, -0.55207), (0.464105, -0.5, 0.731168), (-0.885337, -0.235727, 0.400765)205.98199, 150.08099
42generate(-0.278343, -0.05105, 0.959124), (0.55157, 0.809017, 0.203129), (-0.786318, 0.585564, -0.197026)205.98199, 150.08099
43generate(-0.833065, -0.546575, 0.085196), (0.55157, -0.809017, 0.203129), (-0.042101, 0.216211, 0.975438)205.98199, 150.08099
44generate(-0.856445, 0.463974, 0.226342), (0.464105, 0.5, 0.731168), (0.226072, 0.731251, -0.643555)205.98199, 150.08099
45generate(-0.701741, 0.082601, -0.707628), (0.693092, 0.309017, -0.651254), (0.164875, -0.947463, -0.2741)205.98199, 150.08099
46generate(-0.800129, 0.546575, 0.247081), (0.428354, 0.809017, -0.402497), (-0.419888, -0.216211, -0.881446)205.98199, 150.08099
47generate(-0.630976, 0.05105, -0.774121), (0.428354, -0.809017, -0.402497), (-0.646825, -0.585564, 0.488602)205.98199, 150.08099
48generate(-0.78568, -0.597625, 0.159848), (0.199368, 0.979925), (-0.585628, 0.801776, 0.119147)205.98199, 150.08099
49generate(-0.833065, 0.546575, 0.085196), (-0.55157, -0.809017, -0.203129), (-0.042101, -0.216211, 0.975438)205.98199, 150.08099
50generate(-0.701741, -0.082601, -0.707628), (-0.693092, 0.309017, 0.651254), (0.164875, 0.947463, -0.2741)205.98199, 150.08099
51generate(-0.856445, -0.463974, 0.226342), (-0.464105, 0.5, -0.731168), (0.226072, -0.731251, -0.643555)205.98199, 150.08099
52generate(-0.800129, -0.546575, 0.247081), (-0.428354, 0.809017, 0.402497), (-0.419888, 0.216211, -0.881446)205.98199, 150.08099
53generate(-0.78568, 0.597625, 0.159848), (-0.199368, -0.979925), (-0.585628, -0.801776, 0.119147)205.98199, 150.08099
54generate(-0.630976, -0.05105, -0.774121), (-0.428354, -0.809017, 0.402497), (-0.646825, 0.585564, 0.488602)205.98199, 150.08099
55generate(0.142527, 0.884377, 0.444482), (-0.89246, 0.309017, -0.32867), (-0.428021, -0.349838, 0.833314)205.98199, 150.08099
56generate(0.369464, -0.082601, -0.925567), (-0.89246, -0.309017, -0.32867), (-0.258867, 0.947463, -0.187889)205.98199, 150.08099
57generate(0.119147, -0.801776, 0.585628), (-0.979925, 0.199368), (-0.159848, -0.597625, -0.78568)205.98199, 150.08099
58generate(-0.042476, -0.884377, -0.464837), (-0.693092, -0.309017, 0.651254), (-0.719597, 0.349838, -0.599828)205.98199, 150.08099
59generate(-0.278343, 0.05105, 0.959124), (-0.55157, 0.809017, -0.203129), (-0.786318, -0.585564, -0.197026)205.98199, 150.08099
60generate(-0.028027, 0.833327, -0.55207), (-0.464105, -0.5, -0.731168), (-0.885337, 0.235727, 0.400765)205.98199, 150.08099

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Components

#1: Protein COAT PROTEIN VP2


Mass: 64818.656 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MURINE MINUTE VIRUS / Strain: IMMUNOSUPRESSIVE STRAIN MVMI / Plasmid: PFASTBAC / Cell line (production host): SF1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P07302
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 303 TO TRP ENGINEERED RESIDUE IN CHAIN B, LEU 303 TO TRP

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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: 8 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 10 MM TRIS-HCL, 8 MM CACL2, PEG 8000, VIRUS CONCENTRATION 10 MG/ML, PH 7.5, VAPOR DIFFUSION, HANGING DROP.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.033
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 4.2→35 Å / Num. obs: 214730 / % possible obs: 55.3 % / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.52
Reflection shellResolution: 4.2→4.39 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 1.86 / % possible all: 29.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
GLRFphasing
CNSphasing
CNS1.21refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MVM

1mvm


Resolution: 4.2→35 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Cross valid method: NONE / σ(F): 0 / Stereochemistry target values: CRYSTALLOGRAPHIC RESIDUAL
RfactorNum. reflection% reflection
Rwork0.3029 --
obs0.3029 214730 55.3 %
Solvent computationSolvent model: DENSITY MODIFICATION / Bsol: 63.3752 Å2 / ksol: 0.65 e/Å3
Displacement parametersBiso mean: 108.5 Å2
Baniso -1Baniso -2Baniso -3
1-40.649 Å20 Å2-25.515 Å2
2---24.397 Å20 Å2
3----16.252 Å2
Refine analyzeLuzzati coordinate error obs: 0.96 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 1.31 Å
Refinement stepCycle: LAST / Resolution: 4.2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4295 0 0 0 4295
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
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
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 4.2→4.39 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.4324 13533 -
obs--29.4 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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