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- PDB-1dnv: PARVOVIRUS (DENSOVIRUS) FROM GALLERIA MELLONELLA -

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Basic information

Entry
Database: PDB / ID: 1dnv
TitlePARVOVIRUS (DENSOVIRUS) FROM GALLERIA MELLONELLA
ComponentsGALLERIA MELLONELLA DENSOVIRUS CAPSID PROTEIN
KeywordsVIRUS / PARVOVIRUS / DENSOVIRUS / CAPSID PROTEIN / VIRAL CAPSID / Icosahedral virus
Function / homology
Function and homology information


phospholipase A2 activity / symbiont entry into host cell via permeabilization of host membrane / arachidonate secretion / T=1 icosahedral viral capsid / phospholipid metabolic process / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / structural molecule activity
Similarity search - Function
Capsid protein VP4 / Capsid protein VP4 / Phospholipase A2-like domain / Phospholipase A2-like domain / Phospholipase A2 domain superfamily / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Biological speciesGalleria mellonella densovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, NCS SYMMETRY AVERAGING / Resolution: 3.6 Å
AuthorsSimpson, A.A. / Chipmann, P.R. / Baker, T.S. / Tijssen, P. / Rossmann, M.G.
Citation
Journal: Structure / Year: 1998
Title: The structure of an insect parvovirus (Galleria mellonella densovirus) at 3.7 A resolution.
Authors: Simpson, A.A. / Chipman, P.R. / Baker, T.S. / Tijssen, P. / Rossmann, M.G.
#1: Journal: Structure / Year: 1998
Title: Functional Implications of the Structure of the Murine Parvovirus, Minute Virus of Mice
Authors: Agbandje-McKenna, M. / Llamas-Saiz, A.L. / Wang, F. / Tattersall, P. / Rossmann, M.G.
#2: Journal: Semin.Virol. / Year: 1995
Title: Densonucleosis Viruses Constitute an Increasingly Diversified Subfamily within the Parvoviruses
Authors: Tijssen, P. / Bergoin, M.
#3: Journal: Virology / Year: 1993
Title: Structure, Sequence, and Function Correlations Among Parvoviruses
Authors: Chapman, M.S. / Rossmann, M.G.
#4: Journal: Proteins / Year: 1993
Title: Structure Determination of Feline Panleukopenia Virus Empty Particles
Authors: Agbandje, M. / McKenna, R. / Rossmann, M.G. / Strassheim, M.L. / Parrish, C.R.
#5: Journal: Science / Year: 1991
Title: The Three-Dimensional Structure of Canine Parvovirus and its Functional Implications
Authors: Tsao, J. / Chapman, M.S. / Agbandje, M. / Keller, W. / Smith, K. / Wu, H. / Luo, M. / Smith, T.J. / Rossmann, M.G. / Compans, R.W. / Parrish, C.R.
History
DepositionJul 22, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_oper_list / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_ncs_oper
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_struct_oper_list.id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _pdbx_validate_peptide_omega.omega / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GALLERIA MELLONELLA DENSOVIRUS CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)47,4301
Polymers47,4301
Non-polymers00
Water00
1
A: GALLERIA MELLONELLA DENSOVIRUS CAPSID PROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)2,845,80260
Polymers2,845,80260
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: GALLERIA MELLONELLA DENSOVIRUS CAPSID PROTEIN
x 5


  • icosahedral pentamer
  • 237 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)237,1505
Polymers237,1505
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: GALLERIA MELLONELLA DENSOVIRUS CAPSID PROTEIN
x 6


  • icosahedral 23 hexamer
  • 285 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)284,5806
Polymers284,5806
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: GALLERIA MELLONELLA DENSOVIRUS CAPSID PROTEIN
x 30


  • crystal asymmetric unit, crystal frame
  • 1.42 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)1,422,90130
Polymers1,422,90130
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)264.440, 264.440, 683.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.65314676, 0.28454888, 0.70172802), (0.40372175, 0.65315784, -0.64062961), (-0.64062103, 0.70173054, 0.31172937)-117.80731, 106.97361, 122.0411
3generate(0.09193754, 0.8641315, 0.49479019), (0.93778439, 0.09194439, -0.33483246), (-0.33481606, 0.49480283, -0.8019159)-78.67389, 51.09974, 310.62139
4generate(0.09194439, 0.93778439, -0.33483246), (0.8641315, 0.09193754, 0.49479019), (0.49480283, -0.33481606, -0.8019159)63.3192, -90.40581, 305.12931
5generate(0.65315784, 0.40372175, -0.64062961), (0.28454888, 0.65314676, 0.70172802), (0.70173054, -0.64062103, 0.31172937)111.94234, -121.98719, 113.15474
6generate(-0.33407704, 0.66592296, 0.66703278), (0.66592296, -0.33407704, 0.66703278), (0.66704239, 0.66704239, -0.33184593)-107.34922, -120.58922, 227.55919
7generate(-0.37666898, 0.80796883, -0.45310748), (-0.12724397, 0.43935987, 0.88925016), (0.91756358, 0.39262372, -0.06269089)84.6491, -153.37182, 179.83381
8generate(0.37044465, 0.10259109, -0.92317485), (-0.47540221, 0.87477821, -0.09355221), (0.79797553, 0.47354484, 0.37281111)160.15706, 17.14343, 106.08763
9generate(0.87477821, -0.47540221, -0.09355221), (0.10259109, 0.37044465, -0.92317485), (0.47354484, 0.79797553, 0.37281111)14.82523, 155.31025, 108.23536
10generate(0.43935987, -0.12724397, 0.88925016), (0.80796883, -0.37666898, -0.45310748), (0.39262372, 0.91756358, -0.06269089)-150.50274, 70.18679, 183.30892
11generate(0.93285044, 0.35486399, -0.06217969), (0.11680832, -0.46117813, -0.87958181), (-0.34079219, 0.81325739, -0.47167231)12.02089, 145.06221, 255.26984
12generate(0.79238817, 0.45359036, 0.40788768), (0.45358394, -0.88521386, 0.10322056), (0.40790558, 0.10322654, -0.90717431)-67.50311, -25.37768, 324.85132
13generate(0.43936864, 0.80796652, 0.39260814), (-0.12724847, -0.37668456, 0.91756366), (0.88925196, -0.45309961, -0.06268408)-62.55097, -160.91056, 177.12702
14generate(0.36165283, 0.92825666, -0.08690251), (-0.82299825, 0.36163956, 0.43805301), (0.43804261, -0.08689725, 0.89474159)20.03362, -74.23459, 16.2469
15generate(0.66664135, 0.64822389, -0.36797685), (-0.67216287, 0.30941966, -0.67264397), (-0.32216648, 0.69575442, 0.64197296)66.12156, 114.86699, 64.54182
16generate(-0.46117813, 0.11680832, -0.87958181), (0.35486399, 0.93285044, -0.06217969), (0.81325739, -0.34079219, -0.47167231)155.50848, 9.22716, 247.63003
17generate(0.30941966, -0.67216287, -0.67264397), (0.64822389, 0.66664135, -0.36797685), (0.69575442, -0.32216648, 0.64197296)114.98891, 59.62349, 57.80318
18generate(0.36163956, -0.82299825, 0.43805301), (0.92825666, 0.36165283, -0.08690251), (-0.08689725, 0.43804261, 0.89474159)-75.45689, 9.6627, 19.722
19generate(-0.37668456, -0.12724847, 0.91756366), (0.80796652, 0.43936864, 0.39260814), (-0.45309961, 0.88925196, -0.06268408)-152.63929, -71.61109, 186.01338
20generate(-0.88521386, 0.45358394, 0.10322056), (0.45359036, 0.79238817, 0.40788768), (0.10322654, 0.40790558, -0.90717431)-9.89484, -71.88027, 326.86829
21generate(0.93285136, 0.11681143, -0.34080783), (0.35484986, -0.46119007, 0.81325518), (-0.06217068, -0.87958239, -0.47166129)58.83933, -144.96387, 248.74242
22generate(0.87477682, 0.10258285, 0.47353528), (-0.4754118, 0.37042821, 0.79797564), (-0.09355697, -0.92317587, 0.37282895)-80.1542, -136.85239, 104.41241
23generate(0.30941592, 0.64821373, 0.69575266), (-0.67216373, 0.66663407, -0.32216462), (-0.67265468, -0.36797564, 0.64198398)-114.44488, 56.16647, 62.1791
24generate(0.0180782, 0.99966074, 0.01874745), (0.03649855, 0.01808109, -0.99916983), (-0.99917044, 0.01875045, -0.03615929)3.35585, 167.3472, 180.40749
25generate(0.40338249, 0.67123605, -0.62188216), (0.67122785, -0.67895257, -0.29744181), (-0.62187058, -0.2974399, -0.72442992)110.45138, 43.04181, 295.70996
26generate(-0.46119007, 0.35484986, 0.81325518), (0.11681143, 0.93285136, -0.34080783), (-0.87958239, -0.06217068, -0.47166129)-132.94169, 57.62152, 254.15368
27generate(-0.67895257, 0.67122785, -0.29744181), (0.67123605, 0.40338249, -0.62188216), (-0.2974399, -0.62187058, -0.72442992)58.6, 102.05819, 293.56223
28generate(0.01808109, 0.03649855, -0.99916983), (0.99966074, 0.0180782, 0.01874745), (0.01875045, -0.99917044, -0.03615929)174.08912, -9.76223, 173.66886
29generate(0.66663407, -0.67216373, -0.32216462), (0.64821373, 0.30941592, 0.69575266), (-0.36797564, -0.67265468, 0.64198398)53.92363, -123.30772, 60.16213
30generate(0.37042821, -0.4754118, 0.79797564), (0.10258285, 0.87477682, 0.47353528), (-0.92317587, -0.09355697, 0.37282895)-135.83185, -81.66228, 109.90449

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Components

#1: Protein GALLERIA MELLONELLA DENSOVIRUS CAPSID PROTEIN


Mass: 47430.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PURIFIED FROM WAX MOTH CATERPILLAR / Source: (natural) Galleria mellonella densovirus / Genus: Densovirus / Cellular location: NUCLEUS / Tissue: ALL LARVAL TISSUES, EXCEPT MIDGUT / References: UniProt: Q90125
Compound detailsCAPSID CONTAINS DISORDERED SSDNA AND THE DISORDERED AMINO TERMINAL REGIONS OF THE CAPSID PROTEINS.

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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: 2.2 Å3/Da / Density % sol: 40 % / Description: INITIAL MODEL AT 25A RESOLUTION
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
Conc.: 5 % / Common name: PEG8000

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 1, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3.5→60 Å / Num. obs: 107965 / % possible obs: 35.6 % / Redundancy: 1.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10
Reflection shellResolution: 3.5→3.58 Å / Redundancy: 1.14 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.5 / % possible all: 15.2
Reflection
*PLUS
Num. measured all: 164912
Reflection shell
*PLUS
% possible obs: 15.2 %

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Processing

Software
NameVersionClassification
GLRFphasing
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, NCS SYMMETRY AVERAGING
Starting model: CRYO-EM RECONSTRUCTION

Resolution: 3.6→9 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 2 / Details: THERMAL FACTOR RMS VALUES ARE FOR ALL ATOMS
RfactorNum. reflection% reflection
Rwork0.271 --
obs0.271 93725 35.6 %
Displacement parametersBiso mean: 26.4 Å2
Baniso -1Baniso -2Baniso -3
1--11.185 Å20 Å20 Å2
2---11.185 Å20 Å2
3---22.3701 Å2
Refinement stepCycle: LAST / Resolution: 3.6→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3199 0 0 0 3199
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.71.5
X-RAY DIFFRACTIONx_mcangle_it2.32
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 3.6→3.75 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.42 5842 -
obs--19 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2

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