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- PDB-1k3v: Porcine Parvovirus Capsid -

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Basic information

Entry
Database: PDB / ID: 1k3v
TitlePorcine Parvovirus Capsid
Componentscapsid protein VP2
KeywordsVIRUS / capsid / icosahadral / beta sheet / Icosahedral virus
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
Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / 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 / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Biological speciesPorcine parvovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsSimpson, A.A. / Hebert, B. / Sullivan, G.M. / Parrish, C.R. / Zadori, Z. / Tijssen, P. / Rossmann, M.G.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The structure of porcine parvovirus: comparison with related viruses.
Authors: Simpson, A.A. / Hebert, B. / Sullivan, G.M. / Parrish, C.R. / Zadori, Z. / Tijssen, P. / Rossmann, M.G.
History
DepositionOct 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: capsid protein VP2


Theoretical massNumber of molelcules
Total (without water)64,4111
Polymers64,4111
Non-polymers00
Water0
1
A: capsid protein VP2
x 60


Theoretical massNumber of molelcules
Total (without water)3,864,67960
Polymers3,864,67960
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: capsid protein VP2
x 5


  • icosahedral pentamer
  • 322 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)322,0575
Polymers322,0575
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: capsid protein VP2
x 6


  • icosahedral 23 hexamer
  • 386 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)386,4686
Polymers386,4686
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: capsid protein VP2
x 60


  • crystal asymmetric unit, crystal frame
  • 3.86 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)3,864,67960
Polymers3,864,67960
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)442.49, 443.05, 251.31
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.77978251, -0.34895739, 0.51977685), (0.6228703, 0.34886076, -0.70023479), (0.06302236, 0.8697844, 0.48939072)24.06785, 45.94908, -60.47825
3generate(0.42346313, 0.05824538, 0.90403897), (0.65886793, -0.70470466, -0.26321928), (0.62174917, 0.70710594, -0.33679246)-4.63393, 119.31903, -48.59313
4generate(0.42346313, 0.65886793, 0.62174917), (0.05824538, -0.70470466, 0.70710594), (0.90403897, -0.26321928, -0.33679246)-46.44045, 118.71508, 19.23052
5generate(0.77978251, 0.6228703, 0.06302236), (-0.34895739, 0.34886076, 0.8697844), (0.51977685, -0.70023479, 0.48939072)-43.57652, 44.97186, 49.26273
6generate(-0.58174013, 0.08009324, 0.8094217), (0.08009324, -0.98466282, 0.15499743), (0.8094217, 0.15499743, 0.56640295)103.28968, 180.14758, -71.19964
7generate(-0.35273142, 0.93496628, 0.03766435), (-0.54109362, -0.236645, 0.80698007), (0.76341224, 0.26426728, 0.58937642)44.01625, 127.45693, -78.85166
8generate(0.30968264, 0.48202114, -0.81960495), (-0.5184767, 0.80816114, 0.27938768), (0.79704365, 0.33842456, 0.50019021)76.20973, 54.75561, -83.97959
9generate(0.49006832, -0.65278739, -0.57766916), (0.11668819, 0.70586904, -0.69866499), (0.86383847, 0.27498641, 0.42209663)155.37983, 62.51438, -79.49679
10generate(-0.06086125, -0.9011925, 0.42912468), (0.48662475, -0.40215711, -0.7755424), (0.87148853, 0.16162221, 0.46301836)172.11615, 140.01088, -71.59834
11generate(0.37806724, 0.52305442, -0.76385813), (0.52305442, -0.80147128, -0.28992734), (-0.76385813, -0.28992734, -0.57659596)61.4276, 144.77226, 209.95408
12generate(0.57246515, -0.61384808, -0.54357538), (-0.10961588, -0.71429986, 0.6912019), (-0.81256878, -0.3361045, -0.47619927)140.75753, 138.06849, 213.11928
13generate(0.02979316, -0.88670684, 0.46137117), (-0.48683154, 0.39025671, 0.78146961), (-0.87298764, -0.24789249, -0.42004987)159.20427, 60.80617, 206.9185
14generate(-0.49999447, 0.08155968, 0.86217953), (-0.08729335, 0.9857388, -0.14387111), (-0.8616179, -0.1471973, -0.48574433)91.27504, 19.7592, 199.92101
15generate(-0.28474925, 0.95284005, 0.10494619), (0.5368505, 0.24921039, -0.80603084), (-0.79417215, -0.17317627, -0.58249513)30.84573, 71.65311, 201.7971
16generate(-0.79632711, -0.60314765, -0.04556358), (-0.60314765, 0.7861341, 0.13492991), (-0.04556358, 0.13492991, -0.98980699)249.09145, 75.05799, 119.87913
17generate(-0.99951624, 0.0278392, -0.01386582), (0.0278392, 0.60208411, -0.79794718), (-0.01386582, -0.79794718, -0.60256786)204.96709, 88.50334, 184.84421
18generate(-0.76293894, 0.34644031, -0.54580518), (0.34644031, -0.49371319, -0.79763801), (-0.54580518, -0.79763801, 0.25665213)183.02865, 165.09703, 184.2878
19generate(-0.41353699, -0.08764022, -0.90625954), (-0.08764022, -0.98690317, 0.13543017), (-0.90625954, 0.13543017, 0.40044016)213.59431, 198.98918, 118.97884
20generate(-0.43417202, -0.67451786, -0.59709323), (-0.67451786, -0.19591404, 0.71178884), (-0.59709323, 0.71178884, -0.36991394)254.42336, 143.342, 79.17209
21generate(0.79043074, -0.61241884, 0.01274406), (-0.25893281, -0.35290693, -0.89911651), (0.55513336, 0.70738947, -0.43752382)82.09488, 220.20579, -35.2168
22generate(0.23570972, -0.47839097, 0.8459214), (-0.47839097, -0.81479638, -0.32748885), (0.8459214, -0.32748885, -0.42091335)72.20802, 252.13508, 37.10863
23generate(-0.06086125, 0.48662475, 0.87148853), (-0.9011925, -0.40215711, 0.16162221), (0.42912468, -0.7755424, 0.46301836)4.73958, 222.98804, 67.87643
24generate(0.31056883, 0.94900939, 0.05411255), (-0.94304006, 0.31475743, -0.10771819), (-0.1192579, -0.01757639, 0.99270772)-27.07135, 173.0449, 14.56654
25generate(0.83669622, 0.2697631, -0.47662072), (-0.54610174, 0.34519572, -0.76329077), (-0.04138025, 0.89892591, 0.43614205)20.73685, 171.32537, -49.14858
26generate(-0.49856057, 0.66830951, 0.55208673), (-0.60539827, 0.18739482, -0.77354775), (-0.62042751, -0.71989275, 0.31116575)52.50507, 193.90214, 180.70878
27generate(0.06229514, 0.88731978, -0.45692769), (-0.40410712, -0.39618687, -0.82445946), (-0.91258794, 0.23600755, 0.33389173)37.82476, 234.72494, 113.87926
28generate(0.57246515, -0.10961588, -0.81256878), (-0.61384808, -0.71429986, -0.3361045), (-0.54357538, 0.6912019, -0.47619927)107.72979, 256.65639, 82.56637
29generate(0.32691183, -0.94476627, -0.02335264), (-0.94476627, -0.32732282, 0.01662717), (-0.02335264, 0.01662717, -0.99958901)165.61378, 229.38797, 130.04347
30generate(-0.33501846, -0.46398194, 0.82005085), (-0.939544, 0.22995514, -0.25372763), (-0.07084987, -0.85547729, -0.51297066)131.48302, 190.60372, 190.69882
31generate(-0.03122706, 0.90057955, -0.43356815), (0.40431391, 0.40808727, 0.81853225), (0.91408705, -0.14973728, -0.37686021)44.66354, -35.56414, 9.43417
32generate(0.50926945, -0.05203704, -0.85903246), (0.62104819, 0.71322389, 0.32497819), (0.59577157, -0.69900203, 0.39554065)111.51422, -56.58534, 47.34583
33generate(0.31056883, -0.94304006, -0.1192579), (0.94900939, 0.31475743, -0.01757639), (0.05411255, -0.10771819, 0.99270772)173.33296, -28.52017, 5.64467
34generate(-0.35273142, -0.54109362, 0.76341224), (0.93496628, -0.236645, 0.26426728), (0.03766435, 0.80698007, 0.58937642)144.68837, 9.84625, -58.03973
35generate(-0.5639729, 0.59832596, 0.56915781), (0.59832596, -0.17896399, 0.78101084), (0.56915781, 0.78101084, -0.25706311)65.1663, 5.49283, -55.69769
36generate(-0.26064311, -0.95647023, -0.13126263), (0.46001717, -0.24257516, 0.85413201), (-0.84879289, 0.16224056, 0.50321827)234.54523, 21.43405, 103.70743
37generate(-0.80727432, -0.35689178, 0.47003876), (0.26144989, 0.49775936, 0.82697012), (-0.52910503, 0.79048332, -0.30851903)192.26172, -30.29684, 60.29986
38generate(-0.82217273, 0.56603119, 0.06033814), (0.56603119, 0.80169954, 0.19205868), (0.06033814, 0.19205868, -0.97952681)128.00639, -51.14642, 102.54611
39generate(-0.28474925, 0.5368505, -0.79417215), (0.95284005, 0.24921039, -0.17317627), (0.10494619, -0.80603084, -0.58249513)130.57793, -12.30128, 172.0633
40generate(0.06229514, -0.40410712, -0.91258794), (0.88731978, -0.39618687, 0.23600755), (-0.45692769, -0.82445946, 0.33389173)196.42256, 32.55591, 172.78104
41generate(0.79043074, -0.25893281, 0.55513336), (-0.61241884, -0.35290693, 0.70738947), (0.01274406, -0.89911651, -0.43752382)11.67821, 152.90059, 181.53625
42generate(0.49006832, 0.11668819, 0.86383847), (-0.65278739, 0.70586904, 0.27498641), (-0.57766916, -0.69866499, 0.42209663)-14.76904, 79.16357, 166.99007
43generate(0.50926945, 0.62104819, 0.59577157), (-0.05203704, 0.71322389, -0.69900203), (-0.85903246, 0.32497819, 0.39554065)-49.85587, 79.25572, 95.45614
44generate(0.82149882, 0.55713882, 0.121392), (0.35961565, -0.34100652, -0.86855693), (-0.44251132, 0.75717295, -0.4804923)-45.09347, 153.0497, 65.79192
45generate(0.99526605, 0.01328065, 0.0962762), (0.01328065, -0.9999116, 0.00064082), (0.0962762, 0.00064082, -0.99535445)-7.06332, 198.56473, 118.99236
46generate(-0.03122706, 0.40431391, 0.91408705), (0.90057955, 0.40808727, -0.14973728), (-0.43356815, 0.81853225, -0.37686021)7.15014, -24.29715, 52.03045
47generate(0.28509274, 0.94700483, 0.14799995), (0.94700483, -0.30213741, 0.10906346), (0.14799995, 0.10906346, -0.98295533)-30.30596, 25.18494, 101.99805
48generate(0.82149882, 0.35961565, -0.44251132), (0.55713882, -0.34100652, 0.75717295), (0.121392, -0.86855693, -0.4804923)11.11884, 27.49841, 170.01887
49generate(0.83669622, -0.54610174, -0.04138025), (0.2697631, 0.34519572, 0.89892591), (-0.47662072, -0.76329077, 0.43614205)74.17686, -20.55389, 162.09045
50generate(0.30968264, -0.5184767, 0.79704365), (0.48202114, 0.80816114, 0.33842456), (-0.81960495, 0.27938768, 0.50019021)71.72407, -52.56531, 89.1696
51generate(-0.26064311, 0.46001717, -0.84879289), (-0.95647023, -0.24257516, 0.16224056), (-0.13126263, 0.85413201, 0.50321827)139.2987, 212.70935, -39.70795
52generate(0.02979316, -0.48683154, -0.87298764), (-0.88670684, 0.39025671, -0.24789249), (0.46137117, 0.78146961, -0.42004987)205.49645, 168.73104, -34.05434
53generate(-0.33501846, -0.939544, -0.07084987), (-0.46398194, 0.22995514, -0.85547729), (0.82005085, -0.25372763, -0.51297066)236.64081, 180.31395, 38.36156
54generate(-0.85092072, -0.27248697, 0.44909328), (-0.27248697, -0.50194855, -0.8208523), (0.44909328, -0.8208523, 0.35286927)189.69132, 231.4509, 77.46344
55generate(-0.80495422, 0.5924894, -0.03170195), (-0.57686147, -0.79398834, -0.19186808), (-0.13885078, -0.13615739, 0.98090857)129.53059, 251.47236, 29.21382
56generate(-0.49856057, -0.60539827, -0.62042751), (0.66830951, 0.18739482, -0.71989275), (0.55208673, -0.77354775, 0.31116575)255.68168, 58.66505, 64.77483
57generate(-0.80495422, -0.57686147, -0.13885078), (0.5924894, -0.79398834, -0.13615739), (-0.03170195, -0.19186808, 0.98090857)253.38727, 126.89829, 23.6998
58generate(-0.99574981, -0.04111985, -0.08241038), (-0.04111985, -0.6021725, 0.79730636), (-0.08241038, 0.79730636, 0.59792231)215.90495, 112.90976, -45.20299
59generate(-0.80727432, 0.26144989, -0.52910503), (-0.35689178, 0.49775936, 0.79048332), (0.47003876, 0.82697012, -0.30851903)195.03401, 36.03113, -46.71222
60generate(-0.49999447, -0.08729335, -0.8616179), (0.08155968, 0.9857388, -0.1471973), (0.86217953, -0.14387111, -0.48574433)219.61738, 2.50606, 21.2578

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Components

#1: Protein capsid protein VP2 / / COAT PROTEIN VP2


Mass: 64411.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine parvovirus / Genus: ParvovirusParvoviridae / Gene: VP2 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): High Five / References: UniProt: P18546

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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: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20mM Hepes-NaOH 8mM CaCl, .05% sodium azide, 1-1.5% PEG8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein11
220 mMHEPES-NaOH12pH6.5
38 mM12CaCl2
40.05 %(w/v)sodium azide12
51.0 PEG800012or 1.5%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2001
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. all: 254870 / Num. obs: 254870 / % possible obs: 41.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.46 % / Rmerge(I) obs: 0.29 / Net I/σ(I): 1.8
Reflection shellResolution: 3.5→3.62 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 0.9 / Num. unique all: 17511 / % possible all: 28.6
Reflection shell
*PLUS
Highest resolution: 3.5 Å / % possible obs: 28.6 %

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Processing

Software
NameVersionClassification
AMoRE+ DMphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Feline Panleukopenia virus

Resolution: 3.5→50 Å / Isotropic thermal model: Isotropic / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 3847 -RANDOM
Rwork0.286 ---
all0.394 254870 --
obs0.283 194195 31.4 %-
Refinement stepCycle: LAST / Resolution: 3.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4306 0 0 0 4306
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.67
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_improper_angle_d1.14
LS refinement shellResolution: 3.5→3.52 Å
RfactorNum. reflection
Rfree0.3872 28
Rwork0.3863 -
obs-1921
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 50 Å / σ(F): 1 / Rfactor obs: 0.275
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.14
LS refinement shell
*PLUS
Highest resolution: 3.5 Å / Rfactor obs: 0.377

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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