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- PDB-4mgu: Crystal structure of Acheta domesticus Densovirus -

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Basic information

Entry
Database: PDB / ID: 4mgu
TitleCrystal structure of Acheta domesticus Densovirus
Components
  • DNA (5'-D(P*TP*TP*T)-3')
  • Structural protein VP2Structure
KeywordsVIRUS/DNA / Virus / Jelly-Roll / DNV / VIRUS-DNA complex
Function / homologyCapsid protein VP4 / Capsid protein VP4 / Capsid/spike protein, ssDNA virus / viral capsid / structural molecule activity / DNA / Structural protein VP2
Function and homology information
Biological speciesAcheta domestica densovirus
Acheta domesticus (house cricket)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsMeng, G. / Rossmann, M.G.
CitationJournal: J Virol / Year: 2013
Title: The structure and host entry of an invertebrate parvovirus.
Authors: Geng Meng / Xinzheng Zhang / Pavel Plevka / Qian Yu / Peter Tijssen / Michael G Rossmann /
Abstract: The 3.5-Å resolution X-ray crystal structure of mature cricket parvovirus (Acheta domesticus densovirus [AdDNV]) has been determined. Structural comparisons show that vertebrate and invertebrate ...The 3.5-Å resolution X-ray crystal structure of mature cricket parvovirus (Acheta domesticus densovirus [AdDNV]) has been determined. Structural comparisons show that vertebrate and invertebrate parvoviruses have evolved independently, although there are common structural features among all parvovirus capsid proteins. It was shown that raising the temperature of the AdDNV particles caused a loss of their genomes. The structure of these emptied particles was determined by cryo-electron microscopy to 5.5-Å resolution, and the capsid structure was found to be the same as that for the full, mature virus except for the absence of the three ordered nucleotides observed in the crystal structure. The viral protein 1 (VP1) amino termini could be externalized without significant damage to the capsid. In vitro, this externalization of the VP1 amino termini is accompanied by the release of the viral genome.
History
DepositionAug 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Dec 18, 2013Group: Refinement description
Revision 1.3Feb 28, 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Structural protein VP2
C: DNA (5'-D(P*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)47,7152
Polymers47,7152
Non-polymers00
Water0
1
A: Structural protein VP2
C: DNA (5'-D(P*TP*TP*T)-3')
x 60


Theoretical massNumber of molelcules
Total (without water)2,862,908120
Polymers2,862,908120
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: Structural protein VP2
C: DNA (5'-D(P*TP*TP*T)-3')
x 5


  • icosahedral pentamer
  • 239 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)238,57610
Polymers238,57610
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Structural protein VP2
C: DNA (5'-D(P*TP*TP*T)-3')
x 6


  • icosahedral 23 hexamer
  • 286 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)286,29112
Polymers286,29112
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: Structural protein VP2
C: DNA (5'-D(P*TP*TP*T)-3')
x 30


  • crystal asymmetric unit, crystal frame
  • 1.43 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,431,45460
Polymers1,431,45460
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)415.469, 415.469, 281.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.551285, 0.761738, 0.340327), (-0.276703, 0.55175, -0.786734), (-0.78706, 0.339571, 0.514965)-194.704, 169.0854, -27.6206
3generate(0.566192, -0.223188, 0.793446), (0.737798, 0.566419, -0.367156), (-0.367505, 0.793284, 0.485389)114.031, 62.1982, -212.827
4generate(0.96346, -0.142203, -0.22686), (-0.166478, 0.345427, -0.923551), (0.209695, 0.927598, 0.309112)48.4755, 222.9631, -313.3188
5generate(0.345641, -0.142971, 0.927401), (-0.166566, 0.963253, 0.210576), (-0.923455, -0.227258, 0.309106)110.9964, 28.3655, 164.6719
6generate(0.39725, 0.713576, -0.577013), (-0.90417, 0.411906, -0.113091), (0.157005, 0.566644, 0.808843)-164.0063, 276.3861, -194.3117
7generate(0.412172, 0.713247, 0.566865), (-0.90408, 0.397244, 0.15754), (-0.112845, -0.577425, 0.808584)-165.4068, 280.9955, 193.256
8generate(0.39725, -0.90417, 0.157005), (0.713576, 0.411907, 0.566644), (-0.577013, -0.113091, 0.808843)345.5611, 113.3092, 93.7878
9generate(0.412172, -0.90408, -0.112845), (0.713247, 0.397244, -0.577425), (0.566865, 0.15754, 0.808584)344.0284, 117.9608, -106.7658
10generate(0.345641, -0.166566, -0.923455), (-0.142971, 0.963253, -0.227258), (0.927401, 0.210576, 0.309106)118.4287, 25.9869, -159.8152
11generate(0.96346, -0.166478, 0.209695), (-0.142203, 0.345427, 0.927598), (-0.22686, -0.923551, 0.309112)56.1218, 220.5161, 313.7743
12generate(0.566192, 0.737798, -0.367506), (-0.223188, 0.566419, 0.793284), (0.793446, -0.367156, 0.485389)-188.6662, 159.0704, 35.6655
13generate(0.551285, -0.276703, -0.78706), (0.761738, 0.55175, 0.339571), (0.340327, -0.786734, 0.514965)132.3903, 64.4053, 213.5034
14generate(0.749089, 0.578399, 0.322955), (0.539542, -0.249844, -0.804), (-0.384372, 0.776515, -0.499245)-156.8946, 339.2947, -205.8447
15generate(-0.250619, 0.577578, 0.776876), (0.53898, 0.749874, -0.383628), (-0.804135, 0.322602, -0.499255)-55.8603, 24.4541, -20.5543
16generate(0.475721, 0.500408, -0.723382), (-0.523451, -0.499864, -0.690025), (-0.706887, 0.706915, 0.024143)-104.7714, 525.2026, -151.4105
17generate(-0.499842, 0.499313, 0.707704), (-0.524126, 0.476129, -0.706111), (-0.689528, -0.723871, 0.023714)-6.0849, 217.8467, 297.5169
18generate(-0.499866, -0.476279, 0.72339), (0.499709, 0.52359, 0.690032), (-0.707407, 0.706408, -0.023724)301.2151, 99.6894, -151.1985
19generate(0.523988, -0.475571, 0.70659), (0.499998, -0.499854, -0.707211), (0.689521, 0.723863, -0.024133)197.7825, 422.0309, -297.514
20generate(-0.416301, 0.90002, -0.128986), (-0.732308, -0.415987, -0.539094), (-0.538852, -0.129994, 0.832288)-140.7235, 519.8365, 95.2654
21generate(-0.392179, -0.693587, 0.604214), (0.909157, -0.392252, 0.139837), (0.140041, 0.604167, 0.784431)358.809, 346.8923, -204.421
22generate(0.142933, -0.345267, -0.927546), (-0.96343, 0.165967, -0.210241), (0.226532, 0.923703, -0.308899)195.151, 359.8272, -313.7891
23generate(0.167078, -0.3458, 0.923303), (-0.963283, 0.142241, 0.227586), (-0.210031, -0.927453, -0.309319)192.8849, 367.2857, 313.307
24generate(0.142933, -0.96343, 0.226532), (-0.345267, 0.165967, 0.923703), (-0.927546, -0.210241, -0.308899)389.8635, 297.5133, 159.7242
25generate(0.167078, -0.963283, -0.210031), (-0.3458, 0.142241, -0.927453), (0.923303, 0.227586, -0.309319)387.3835, 305.0403, -164.76
26generate(-0.392179, 0.909157, 0.140041), (-0.693588, -0.392252, 0.604167), (0.604214, 0.139837, 0.784431)-146.033, 508.4569, -104.9546
27generate(-0.416301, -0.732308, -0.538852), (0.90002, -0.415987, -0.129994), (-0.128987, -0.539094, 0.832288)373.4371, 355.2896, 182.8095
28generate(-0.499866, 0.499709, -0.707407), (-0.476279, 0.52359, 0.706408), (0.72339, 0.690032, -0.023724)-6.2074, 198.0739, -290.2718
29generate(0.523988, 0.499997, 0.689521), (-0.475571, -0.499854, 0.723863), (0.70659, -0.707211, -0.024133)-109.5078, 520.373, 151.5339
30generate(0.475721, -0.523451, -0.706887), (0.500408, -0.499864, 0.706915), (-0.723382, -0.690025, 0.024143)217.7298, 421.9926, 290.2689
31generate(-0.499842, -0.524126, -0.689528), (0.499313, 0.476129, -0.723871), (0.707704, -0.706111, 0.023714)316.2841, 114.6789, 151.0751
32generate(-0.250619, 0.53898, -0.804135), (0.577578, 0.749874, 0.322602), (0.776876, -0.383628, -0.499255)-43.7025, 20.5633, 42.5245
33generate(0.749089, 0.539542, -0.384372), (0.578399, -0.249844, 0.776515), (0.322955, -0.803999, -0.499245)-144.6551, 335.3777, 220.6931
34generate(-0.1747, 0.955789, -0.236412), (0.314031, -0.17348, -0.933418), (-0.933191, -0.237308, -0.26982)-182.6445, 337.9739, 168.819
35generate(-0.135671, 0.376683, 0.916344), (0.97057, -0.135076, 0.199226), (0.198822, 0.916431, -0.347253)-4.1685, 259.6949, -308.7053
36generate(0.904396, -0.396583, -0.157391), (-0.411584, -0.713691, -0.566733), (0.112454, 0.577331, -0.808705)134.5553, 581.2784, -193.187
37generate(-0.713132, -0.397912, 0.577107), (-0.412494, 0.903853, 0.113481), (-0.566776, -0.157154, -0.808722)298.0288, 71.8663, 106.6351
38generate(-0.577981, 0.250453, -0.77663), (-0.74939, -0.539609, 0.383691), (-0.323006, 0.803765, 0.49959)80.1791, 560.4976, -220.6141
39generate(-0.538913, 0.25001, 0.804369), (-0.749573, -0.577997, -0.322551), (0.38431, -0.776761, 0.49891)76.3804, 572.6077, 205.9284
40generate(-0.577981, -0.74939, -0.323006), (0.250453, -0.539609, 0.803765), (-0.77663, 0.383691, 0.49959)395.1157, 459.7083, -42.5689
41generate(-0.538913, -0.749573, 0.38431), (0.25001, -0.577997, -0.776761), (0.804369, -0.322551, 0.49891)391.2353, 471.8447, 20.5146
42generate(-0.713132, -0.412494, -0.566776), (-0.397911, 0.903853, -0.157154), (0.577107, 0.113481, -0.808722)302.622, 70.3963, -93.9203
43generate(0.904396, -0.411584, 0.112454), (-0.396583, -0.713691, 0.577331), (-0.157391, -0.566733, -0.808705)139.2807, 579.7661, 194.3788
44generate(-0.135671, 0.97057, 0.198822), (0.376683, -0.135076, 0.916431), (0.916344, 0.199226, -0.347253)-191.2347, 319.5617, -155.1254
45generate(-0.1747, 0.314031, -0.933191), (0.955789, -0.17348, -0.237308), (-0.236412, -0.933418, -0.26982)19.5003, 273.2815, 317.8451
46generate(-0.001269, 0.999427, -0.033828), (0.999427, 0.000123, -0.033852), (-0.033828, -0.033852, -0.998854)-213.8725, 214.1998, 14.0729
47generate(0.693139, 0.392835, -0.604303), (0.392835, -0.908845, -0.140224), (-0.604303, -0.140224, -0.784293)-92.8043, 561.6599, 105.0853
48generate(-0.909467, 0.391596, -0.139655), (0.391596, 0.694036, -0.604077), (-0.139655, -0.604077, -0.784569)69.1366, 56.8995, 204.3538
49generate(-0.900267, 0.415644, 0.129377), (0.415644, 0.732434, 0.539188), (0.129377, 0.539188, -0.832166)60.6344, 42.3806, -182.8785
50generate(0.732182, 0.416644, 0.538758), (0.416644, -0.899773, 0.129604), (0.538758, 0.129604, -0.83241)-104.2396, 556.402, -95.1329
51generate(-0.377048, 0.135684, -0.916192), (0.135684, -0.970418, -0.199554), (-0.916192, -0.199554, 0.347466)96.0748, 606.9764, 155.2134
52generate(-0.970722, 0.135063, -0.198493), (0.135063, -0.376318, -0.916583), (-0.198493, -0.916583, 0.34704)156.1157, 419.9058, 308.72
53generate(-0.955838, 0.173973, 0.236747), (0.173973, -0.314188, 0.933273), (0.236747, 0.933273, 0.270027)142.3593, 396.4136, -317.8333
54generate(-0.313873, 0.174207, 0.933335), (0.174207, -0.95574, 0.236973), (0.933336, 0.236973, 0.269613)77.5723, 598.4697, -168.728
55generate(0.223341, -0.565803, -0.79368), (-0.565803, -0.738296, 0.367105), (-0.79368, 0.367105, -0.485045)256.5111, 604.5747, -35.6258
56generate(-0.7373, -0.566808, 0.367556), (-0.566808, 0.223034, -0.79305), (0.367556, -0.79305, -0.485734)353.665, 301.8705, 212.7481
57generate(-0.76146, -0.551707, -0.340265), (-0.551707, 0.276091, 0.786979), (-0.340265, 0.786979, -0.51463)351.3439, 283.6362, -213.5872
58generate(0.277315, -0.551328, 0.786814), (-0.551328, -0.762016, -0.339634), (0.786814, -0.339634, -0.515299)246.5108, 610.587, 27.665
59generate(0.000687, -1, -0.000297), (-1, -0.000687, 0.000297), (-0.000297, 0.000297, -1)415.7216, 416.0073, -0.0635
60generate(-0.999417, 0.000573, 0.034125), (0.000573, -0.999437, 0.033555), (0.034125, 0.033555, 0.998854)201.3708, 629.7368, -14.0094

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Components

#1: Protein Structural protein VP2 / Structure


Mass: 46847.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acheta domestica densovirus / References: UniProt: F2Y986
#2: DNA chain DNA (5'-D(P*TP*TP*T)-3')


Mass: 867.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNV / Source: (natural) Acheta domesticus (house cricket)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 200, 200mM MgCl2, 100mM Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→40 Å / Num. all: 167669 / Num. obs: 306064 / % possible obs: 45 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameClassification
MAR345dtbdata collection
GLRFphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→40 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.29 13228 Random
Rwork0.29 --
all0.29 421816 -
obs0.29 236217 -
Refinement stepCycle: LAST / Resolution: 3.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2946 59 0 0 3005

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