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- PDB-3p0s: Crystal structure of Bombyx mori densovirus 1 capsid -

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Basic information

Entry
Database: PDB / ID: 3p0s
TitleCrystal structure of Bombyx mori densovirus 1 capsid
ComponentsCapsid protein VP
KeywordsVIRUS / icosahedral virus capsid / virus-like particle / capsid protein / beta-barrel
Function / homologyParvovirus non-structural protein 1, helicase domain / Parvovirus non-structural protein NS1 / Capsid/spike protein, ssDNA virus / viral genome replication / ATP binding / Capsid protein VP
Function and homology information
Biological speciesBombyx mori densovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKaufmann, B. / Rossmann, M.G.
CitationJournal: J.Virol. / Year: 2011
Title: Structure of Bombyx mori densovirus 1, a silkworm pathogen.
Authors: Kaufmann, B. / El-Far, M. / Plevka, P. / Bowman, V.D. / Li, Y. / Tijssen, P. / Rossmann, M.G.
History
DepositionSep 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_remark / pdbx_struct_oper_list / 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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][2] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _struct_ncs_oper.matrix[3][3]
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein VP


Theoretical massNumber of molelcules
Total (without water)54,9911
Polymers54,9911
Non-polymers00
Water0
1
A: Capsid protein VP
x 60


Theoretical massNumber of molelcules
Total (without water)3,299,43860
Polymers3,299,43860
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 VP
x 5


  • icosahedral pentamer
  • 275 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)274,9535
Polymers274,9535
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP
x 6


  • icosahedral 23 hexamer
  • 330 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)329,9446
Polymers329,9446
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 VP
x 60


  • crystal asymmetric unit, crystal frame
  • 3.3 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)3,299,43860
Polymers3,299,43860
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)245.400, 245.600, 245.700
Angle α, β, γ (deg.)59.980, 67.930, 72.270
Int Tables number1
Space group name H-MP1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.47978658, -0.03825931, -0.87655038), (-0.53069785, 0.78291778, -0.32465436), (0.69868789, 0.62094737, 0.35532962)
3generate(-0.36193583, -0.59260187, -0.71960037), (-0.89694656, 0.43167113, 0.09564642), (0.25395014, 0.68006042, -0.68776928)
4generate(-0.36193549, -0.89694508, 0.25395045), (-0.59260287, 0.43167097, 0.68006095), (-0.71960081, 0.09564691, -0.68776946)
5generate(0.47978714, -0.53069699, 0.69868794), (-0.03825941, 0.78291752, 0.6209482), (-0.87655062, -0.32465354, 0.35532932)
6generate(-0.59273912, -0.76308356, 0.25760956), (-0.76308505, 0.42979032, -0.48268325), (0.25760951, -0.48268222, -0.83705119)
7generate(0.30056721, -0.41479192, 0.85884042), (-0.93145171, 0.0659647, 0.35783753), (-0.20508153, -0.9075212, -0.3665319)
8generate(0.96439869, 0.19704723, 0.17637314), (-0.23188861, 0.30947992, 0.92219889), (0.12713278, -0.93026524, 0.34415537)
9generate(0.48136279, 0.22689298, -0.84664569), (0.36883183, 0.82380622, 0.43047262), (0.79514356, -0.51948285, 0.31286497)
10generate(-0.48100131, -0.36650048, -0.79643882), (0.04053439, 0.89816214, -0.4377923), (0.87578261, -0.24286133, -0.41716083)
11generate(-0.9071566, -0.08927103, -0.41121492), (-0.08927112, -0.91416379, 0.39539287), (-0.41121462, 0.39539215, 0.82132039)
12generate(-0.6751765, -0.29052751, 0.67803385), (0.71856988, -0.46678148, 0.5155327), (0.1667176, 0.83528907, 0.523924)
13generate(0.30397574, 0.21939598, 0.92707275), (0.95267656, -0.07282484, -0.29513602), (0.00276211, 0.97291341, -0.2311509)
14generate(0.67714502, 0.7358025, -0.00826151), (0.28952146, -0.27672856, -0.91629667), (-0.67650017, 0.61807299, -0.40041646)
15generate(-0.07137593, 0.54503581, -0.83536878), (-0.35443764, -0.79670462, -0.48952635), (-0.93235185, 0.26114522, 0.25004656)
16generate(0.49989572, 0.85235459, 0.15360536), (0.85235617, -0.51562653, 0.08729039), (0.1536051, 0.08729008, -0.9842692)
17generate(-0.10517729, 0.74357875, -0.66032389), (0.74357968, -0.38210101, -0.54871586), (-0.66032396, -0.54871524, -0.51272171)
18generate(-0.9064386, 0.17615866, -0.38384552), (0.1761586, -0.66832621, -0.72270929), (-0.38384502, -0.72270858, 0.57476481)
19generate(-0.79657232, -0.0657504, 0.60095675), (-0.06575041, -0.97874862, -0.19423689), (0.60095742, -0.19423706, 0.77532095)
20generate(0.07259009, 0.35216166, 0.93311965), (0.35216266, -0.88437503, 0.30637045), (0.93311986, 0.30636965, -0.18821505)
21generate(-0.48014324, 0.53269484, -0.69692075), (-0.22484001, 0.6932133, 0.68476475), (0.84788557, 0.48548006, -0.21307006)
22generate(-0.99999638, 0.00267511, 0.00029145), (0.00267481, 0.97653411, 0.21534607), (0.00029142, 0.21534616, -0.97653774)
23generate(-0.48100088, 0.04053455, 0.87578228), (-0.36650152, 0.89816218, -0.24286183), (-0.79643902, -0.43779136, -0.4171613)
24generate(0.35960911, 0.59395269, 0.71965317), (-0.82217988, 0.56640483, -0.05663121), (-0.44125137, -0.57131864, 0.69202004)
25generate(0.36013917, 0.89812448, -0.25233076), (-0.73462824, 0.43973945, 0.51667354), (0.57499711, -0.00070553, 0.81815536)
26generate(-0.3014252, 0.93172775, 0.20254597), (-0.21930732, 0.13898431, -0.96570654), (-0.9279264, -0.33550778, 0.16244088)
27generate(-0.49756926, 0.86676894, 0.03369548), (-0.85370685, -0.4824491, -0.19603208), (-0.1536579, -0.12630594, 0.98001836)
28generate(-0.67517684, 0.71856861, 0.16671721), (-0.29052763, -0.46678135, 0.83529026), (0.67803425, 0.51553151, 0.52392421)
29generate(-0.58880032, 0.69193457, 0.41777965), (0.6919358, 0.16433527, 0.70300807), (0.41777978, 0.70300703, -0.57553495)
30generate(-0.35780909, 0.82367416, 0.43992305), (0.73595237, 0.53871903, -0.41006916), (-0.57475849, 0.17703583, -0.79894393)
31generate(0.67459483, -0.71966444, -0.16432941), (-0.1395041, -0.34288819, 0.92896041), (-0.72488682, -0.60374614, -0.33170663)
32generate(0.59077095, -0.69128755, -0.41606526), (0.76409122, 0.31371959, 0.56368967), (-0.25914359, -0.65092228, 0.71354344)
33generate(0.35960903, -0.82217845, -0.44125129), (0.59395355, 0.56640466, -0.57131925), (0.7196536, -0.05663105, 0.69202029)
34generate(0.30056699, -0.93145036, -0.20508126), (-0.41479264, 0.06596483, -0.9075226), (0.85884032, 0.35783727, -0.36653182)
35generate(0.49523891, -0.86809322, -0.03393413), (-0.8680944, -0.49600905, 0.01970122), (-0.03393475, 0.01970156, -0.99922986)
36generate(0.10697361, -0.74475815, 0.65870419), (0.58365143, -0.48930941, -0.64801862), (0.80492765, 0.45377386, 0.38233581)
37generate(0.90679469, -0.1781565, 0.38207833), (0.08694082, -0.80780461, -0.58300366), (0.41251007, 0.56188206, -0.71702406)
38generate(0.7965687, 0.06307529, -0.6012482), (0.06307561, -0.99778549, -0.02110918), (-0.60124884, -0.0211091, -0.79878321)
39generate(-0.07137579, -0.3544369, -0.93235156), (0.54503672, -0.79670493, 0.26114574), (-0.83536873, -0.48952566, 0.25004673)
40generate(-0.497569, -0.85370542, -0.15365816), (0.86677026, -0.48244943, -0.1263056), (0.03369613, -0.19603185, 0.98001843)
41generate(-0.48014263, -0.2248398, 0.84788538), (0.53269547, 0.69321319, 0.48548083), (-0.6969209, 0.68476424, -0.21307056)
42generate(0.48136325, 0.36883105, 0.79514321), (0.22689296, 0.82380642, -0.51948339), (-0.84664603, 0.43047221, 0.3128643)
43generate(0.59077072, 0.76408985, -0.25914382), (-0.69128885, 0.31372008, -0.6509233), (-0.41606558, 0.56368873, 0.71354317)
44generate(-0.30311763, 0.41470238, -0.85798688), (-0.95295392, -0.13212384, 0.27280659), (-0.00022711, 0.90031307, 0.43524146)
45generate(-0.96497848, -0.19648976, -0.17380521), (-0.19649, 0.1024158, 0.97514296), (-0.17380523, 0.97514186, -0.13743732)
46generate(0.67459455, -0.13950422, -0.72488639), (-0.71966559, -0.34288781, -0.60374726), (-0.16433007, 0.92895929, -0.33170675)
47generate(-0.10877334, -0.58514616, -0.80359906), (-0.58514697, -0.61581432, 0.52761389), (-0.80359956, 0.52761347, -0.27541233)
48generate(-0.30311712, -0.95295248, -0.00022698), (0.41470311, -0.1321242, 0.90031445), (-0.85798688, 0.27280659, 0.43524132)
49generate(0.36013972, -0.73462733, 0.57499695), (0.89812583, 0.43973924, -0.00070509), (-0.25233062, 0.51667308, 0.81815501)
50generate(0.96439876, -0.23188866, 0.1271328), (0.19704742, 0.30948018, -0.93026634), (0.17637287, 0.92219775, 0.34415504)
51generate(0.1069734, 0.58365045, 0.80492731), (-0.74475895, -0.48930937, 0.45377453), (0.65870444, -0.64801825, 0.38233597)
52generate(0.30397533, 0.95267509, 0.00276227), (0.21939685, -0.07282494, 0.97291469), (0.92707296, -0.29513608, -0.23115038)
53generate(-0.35780937, 0.73595161, -0.5747583), (0.82367541, 0.53871891, 0.17703594), (0.43992327, -0.4100687, -0.79894352)
54generate(-0.96381674, 0.2329845, -0.1295206), (0.23298432, 0.50018936, -0.83398433), (-0.1295203, -0.83398312, -0.53637262)
55generate(-0.67656519, 0.1388572, 0.723172), (-0.73636143, -0.13516705, -0.66295048), (0.00569389, -0.98104404, 0.19369826)
56generate(-0.30142532, -0.21930643, -0.92792629), (0.93172907, 0.13898398, -0.3355081), (0.20254653, -0.96570528, 0.16244134)
57generate(-0.67656524, -0.73635997, 0.00569358), (0.13885716, -0.13516716, -0.98104518), (0.72317262, -0.66294961, 0.19369842)
58generate(0.07015577, -0.54708899, 0.83412909), (-0.54708967, -0.72031479, -0.4264271), (0.83412919, -0.42642662, -0.34984097)
59generate(0.90679465, 0.08694046, 0.41251052), (-0.17815622, -0.80780477, 0.56188282), (0.38207803, -0.58300303, -0.71702386)
60generate(0.6771449, 0.28952122, -0.67649959), (0.73580401, -0.27672893, 0.61807385), (-0.00826153, -0.91629557, -0.40041598)

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Components

#1: Protein Capsid protein VP /


Mass: 54990.637 Da / Num. of mol.: 1 / Fragment: VP3 capsid protein residues 179-672
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori densovirus 1 / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): High-Five / References: UniProt: Q8V0M6

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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: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2% PEG8000, 10mM Tris-HCl, 30% glycerol, initial protein concentration in drop 5mg/ml, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.2 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 14, 2004
Details: 162 mm diameter active area, 3 sec read-out, 2048 x 2048 of 0.079mm pixels
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 789029 / Num. obs: 789029 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Χ2: 1.102 / Net I/σ(I): 16.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.1-3.211.30.122631081.639176.6
3.21-3.3420.081806721.157197.8
3.34-3.4920.071801861.231197.1
3.49-3.6820.059804011.22197.4
3.68-3.9120.052802731.232197.2
3.91-4.2120.041805601.089197.8
4.21-4.6320.033811980.967198.2
4.63-5.320.03808540.962198.2
5.3-6.6720.03811800.969198.4
6.67-5020.021805970.951197.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
CNSphasing
AVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→45 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rwork0.2089 ---
all0.2089 788393 --
obs0.2089 788393 95.4 %-
Rfree---None selected, because of icosahedral symmetry averaging
Solvent computationBsol: 3.4267 Å2
Displacement parametersBiso max: 66.97 Å2 / Biso mean: 17.7607 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--1.525 Å2-2.735 Å2-1.29 Å2
2---0.648 Å24.272 Å2
3---2.174 Å2
Refinement stepCycle: LAST / Resolution: 3.1→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3290 0 0 0 3290
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.0981.5
X-RAY DIFFRACTIONc_scbond_it1.8542
X-RAY DIFFRACTIONc_mcangle_it1.8922
X-RAY DIFFRACTIONc_scangle_it2.8952.5
LS refinement shellResolution: 3.1→3.24 Å /
RfactorNum. reflection
Rwork0.3012 -
obs-81860
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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