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- PDB-1z14: Structural Determinants of Tissue Tropism and In Vivo Pathogenici... -

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Basic information

Entry
Database: PDB / ID: 1z14
TitleStructural Determinants of Tissue Tropism and In Vivo Pathogenicity for the Parvovirus Minute Virus of Mice
ComponentsVP2
KeywordsVIRUS / Minute virus of Mice / prototype strain / 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 / T=1 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / structural molecule activity
Similarity search - Function
Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / 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 speciesMinute virus of mice
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsKontou, M. / Govindasamy, L. / Nam, H.J. / Bryant, N. / Llamas-Saiz, A.L. / Foces-Foces, C. / Hernando, E. / Rubio, M.P. / McKenna, R. / Almendral, J.M. / Agbandje-McKenna, M.
CitationJournal: J.Virol. / Year: 2005
Title: Structural determinants of tissue tropism and in vivo pathogenicity for the parvovirus minute virus of mice.
Authors: Kontou, M. / Govindasamy, L. / Nam, H.J. / Bryant, N. / Llamas-Saiz, A.L. / Foces-Foces, C. / Hernando, E. / Rubio, M.P. / McKenna, R. / Almendral, J.M. / Agbandje-McKenna, M.
History
DepositionMar 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Apr 19, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_2 / database_PDB_matrix / diffrn_source / pdbx_struct_assembly_gen / pdbx_struct_oper_list / 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_z ..._atom_site.Cartn_x / _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][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][3] / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly_gen.oper_expression / _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
Remark 999SEQUENCE the authors state that the this difference between the crystal coordinates and GenBank ...SEQUENCE the authors state that the this difference between the crystal coordinates and GenBank sequence database is due to an error in the deposited GenBank sequence or a possible difference in an earlier variant of the virus. Residue 276 is a proline.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP2


Theoretical massNumber of molelcules
Total (without water)61,2461
Polymers61,2461
Non-polymers00
Water2,180121
1
A: VP2
x 60


Theoretical massNumber of molelcules
Total (without water)3,674,76460
Polymers3,674,76460
Non-polymers00
Water1,08160
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: VP2
x 5


  • icosahedral pentamer
  • 306 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)306,2305
Polymers306,2305
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP2
x 6


  • icosahedral 23 hexamer
  • 367 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)367,4766
Polymers367,4766
Non-polymers00
Water1086
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: VP2
x 60


  • crystal asymmetric unit, crystal frame
  • 3.67 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)3,674,76460
Polymers3,674,76460
Non-polymers00
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
transform to crystal frame1
point symmetry operation29
Unit cell
Length a, b, c (Å)448.700, 416.500, 306.100
Angle α, β, γ (deg.)90.00, 95.90, 90.00
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.31417082, -0.83621016, 0.44949901), (0.77346317, 0.5, 0.38955696), (-0.55050099, 0.22528352, 0.80386316)
3generate(-0.79552411, -0.57955319, 0.17680368), (0.41527965, -0.30901699, 0.8555999), (-0.44123031, 0.75407341, 0.48650711)
4generate(-0.7955241, 0.4152797, -0.44123031), (-0.57955311, -0.30901699, 0.75407332), (0.17680368, 0.85560001, 0.48650712)
5generate(0.31417082, 0.77346326, -0.55050099), (-0.83621005, 0.5, 0.22528349), (0.449499, 0.38955701, 0.80386317)
6generate(-0.97938469, -0.20200398), (-1), (-0.20200398, 0.97938469)
7generate(-0.1964907, 0.77346326, -0.602616), (-0.77346317, -0.5, -0.38955696), (-0.602616, 0.38955701, 0.6964907)
8generate(0.86825441, 0.4152797, -0.27143518), (-0.41527965, 0.30901699, -0.8555999), (-0.27143519, 0.85560001, 0.44076257)
9generate(0.74340909, -0.57955319, 0.33385785), (0.57955311, 0.30901699, -0.75407332), (0.33385784, 0.75407341, 0.56560789)
10generate(-0.39849468, -0.83621016, 0.37676869), (0.83621005, -0.5, -0.22528349), (0.37676869, 0.22528352, 0.89849468)
11generate(-0.10100199, -0.1015266, 0.98969235), (0.99483276, 0.10152659), (-0.01030765, 0.99483289, 0.10100199)
12generate(-0.65508558, 0.25665697, 0.71062654), (0.25665693, -0.80901699, 0.52878982), (0.71062654, 0.52878989, 0.46410258)
13generate(-0.39849468, 0.83621016, 0.37676869), (-0.83621005, -0.5, 0.22528349), (0.37676869, -0.22528352, 0.89849468)
14generate(0.31417082, 0.83621016, 0.44949901), (-0.77346317, 0.5, -0.38955696), (-0.55050099, -0.22528352, 0.80386316)
15generate(0.49803141, 0.25665697, 0.82830666), (0.35818352, 0.80901699, -0.46604294), (-0.78972733, 0.52878989, 0.31098558)
16generate(-0.10100199, 0.1015266, 0.98969235), (-0.99483276, -0.10152659), (-0.01030765, -0.99483289, 0.10100199)
17generate(-0.49803141, 0.35818357, 0.78972733), (-0.25665693, 0.80901699, -0.52878982), (-0.82830666, -0.466043, -0.31098558)
18generate(-0.31417082, 0.77346326, 0.55050099), (0.83621005, 0.5, -0.22528349), (-0.449499, 0.38955701, -0.80386317)
19generate(0.1964907, 0.77346326, 0.602616), (0.77346317, -0.5, 0.38955696), (0.602616, 0.38955701, -0.6964907)
20generate(0.32823628, 0.35818357, 0.87405119), (-0.35818352, -0.80901699, 0.46604294), (0.87405119, -0.466043, -0.13725328)
21generate(-0.10100199, 0.99483289, -0.01030765), (-0.10152659, 0.99483276), (0.98969235, 0.1015266, 0.10100199)
22generate(0.74340909, 0.57955319, 0.33385785), (-0.57955311, 0.30901699, 0.75407332), (0.33385784, -0.75407341, 0.56560789)
23generate(0.49803141, -0.25665697, 0.82830666), (-0.35818352, 0.80901699, 0.46604294), (-0.78972733, -0.52878989, 0.31098558)
24generate(-0.49803141, -0.35818357, 0.78972733), (0.25665693, 0.80901699, 0.52878982), (-0.82830666, 0.466043, -0.31098558)
25generate(-0.86825441, 0.4152797, 0.27143518), (0.41527965, 0.30901699, 0.8555999), (0.27143519, 0.85560001, -0.44076257)
26generate(0.10100199, 0.99483289, 0.01030765), (0.10152659, -0.99483276), (-0.98969235, 0.1015266, -0.10100199)
27generate(0.7955241, 0.4152797, 0.44123031), (0.57955311, -0.30901699, -0.75407332), (-0.17680368, 0.85560001, -0.48650712)
28generate(0.32823628, -0.35818357, 0.87405119), (0.35818352, -0.80901699, -0.46604294), (0.87405119, 0.466043, -0.13725328)
29generate(-0.65508558, -0.25665697, 0.71062654), (-0.25665693, -0.80901699, -0.52878982), (0.71062654, -0.52878989, 0.46410258)
30generate(-0.79552411, 0.57955319, 0.17680368), (-0.41527965, -0.30901699, -0.8555999), (-0.44123031, -0.75407341, 0.48650711)
31generate(-0.72236396, -0.69151297), (1), (0.69151297, -0.72236396)-15.732, 208.188, 152.239
32generate(0.1537329, 0.4482616, -0.88058368), (0.77346317, 0.5, 0.38955696), (0.61491527, -0.74098687, -0.26984739)-15.732, 208.188, 152.239
33generate(0.87977442, -0.10280321, -0.46414258), (0.41527965, -0.30901699, 0.8555999), (-0.23138636, -0.945484, -0.22917317)-15.732, 208.188, 152.239
34generate(0.4523959, -0.89164159, -0.01769711), (-0.57955311, -0.30901699, 0.75407332), (-0.67783184, -0.33088332, -0.65655169)-15.732, 208.188, 152.239
35generate(-0.53778007, -0.82810571, -0.15821973), (-0.83621005, 0.5, 0.22528349), (-0.10744868, 0.25345793, -0.96136035)-15.732, 208.188, 152.239
36generate(0.84716057, -0.53133682), (-1), (-0.53133682, -0.84716057)-15.732, 208.188, 152.239
37generate(0.55865458, -0.82810571, -0.04632427), (-0.77346317, -0.5, -0.38955696), (0.29943221, 0.25345793, -0.91983656)-15.732, 208.188, 152.239
38generate(-0.43949474, -0.89164159, -0.10871804), (-0.41527965, 0.30901699, -0.8555999), (0.79648418, -0.33088332, -0.50609195)-15.732, 208.188, 152.239
39generate(-0.76787896, -0.10280321, -0.63229207), (0.57955311, 0.30901699, -0.75407332), (0.27291015, -0.945484, -0.17770773)-15.732, 208.188, 152.239
40generate(0.02731776, 0.4482616, -0.89348484), (0.83621005, -0.5, -0.22528349), (-0.54772836, -0.74098687, -0.38849974)-15.732, 208.188, 152.239
41generate(0.08008807, -0.61460068, -0.78476227), (0.99483276, 0.10152659), (-0.06239831, -0.78883839, 0.6114249)-15.732, 208.188, 152.239
42generate(-0.01819725, -0.55106481, -0.83426395), (0.25665693, -0.80901699, 0.52878982), (-0.96633118, -0.20449713, 0.15615649)-15.732, 208.188, 152.239
43generate(0.02731776, -0.4482616, -0.89348484), (-0.83621005, -0.5, 0.22528349), (-0.54772836, 0.74098687, -0.38849974)-15.732, 208.188, 152.239
44generate(0.1537329, -0.4482616, -0.88058368), (-0.77346317, 0.5, -0.38955696), (0.61491527, 0.74098687, -0.26984739)-15.732, 208.188, 152.239
45generate(0.18634675, -0.55106481, -0.81338944), (0.35818352, 0.80901699, -0.46604294), (0.91486574, -0.20449713, 0.34814002)-15.732, 208.188, 152.239
46generate(0.08008807, 0.61460068, -0.78476227), (-0.99483276, -0.10152659), (-0.06239831, 0.78883839, 0.6114249)-15.732, 208.188, 152.239
47generate(0.93254474, 0.06353587, -0.35542), (-0.25665693, 0.80901699, -0.52878982), (0.2539437, 0.58434124, 0.77075146)-15.732, 208.188, 152.239
48generate(0.53778007, -0.82810571, 0.15821973), (0.83621005, 0.5, -0.22528349), (0.10744868, 0.25345793, 0.96136035)-15.732, 208.188, 152.239
49generate(-0.55865458, -0.82810571, 0.04632427), (0.77346317, -0.5, 0.38955696), (-0.29943221, 0.25345793, 0.91983656)-15.732, 208.188, 152.239
50generate(-0.84152379, 0.06353587, -0.53647065), (-0.35818352, -0.80901699, 0.46604294), (-0.40440343, 0.58434124, 0.70356455)-15.732, 208.188, 152.239
51generate(-0.6114249, -0.78883839, -0.06239831), (-0.10152659, 0.99483276), (-0.78476227, 0.61460068, -0.08008807)-15.732, 208.188, 152.239
52generate(-0.76787896, 0.10280321, -0.63229207), (-0.57955311, 0.30901699, 0.75407332), (0.27291015, 0.945484, -0.17770773)-15.732, 208.188, 152.239
53generate(0.18634675, 0.55106481, -0.81338944), (-0.35818352, 0.80901699, 0.46604294), (0.91486574, 0.20449713, 0.34814002)-15.732, 208.188, 152.239
54generate(0.93254474, -0.06353587, -0.35542), (0.25665693, 0.80901699, 0.52878982), (0.2539437, -0.58434124, 0.77075146)-15.732, 208.188, 152.239
55generate(0.43949474, -0.89164159, 0.10871804), (0.41527965, 0.30901699, 0.8555999), (-0.79648418, -0.33088332, 0.50609195)-15.732, 208.188, 152.239
56generate(0.6114249, -0.78883839, 0.06239831), (0.10152659, -0.99483276), (0.78476227, 0.61460068, 0.08008807)-15.732, 208.188, 152.239
57generate(-0.4523959, -0.89164159, 0.01769711), (0.57955311, -0.30901699, -0.75407332), (0.67783184, -0.33088332, 0.65655169)-15.732, 208.188, 152.239
58generate(-0.84152379, -0.06353587, -0.53647065), (0.35818352, -0.80901699, -0.46604294), (-0.40440343, -0.58434124, 0.70356455)-15.732, 208.188, 152.239
59generate(-0.01819725, 0.55106481, -0.83426395), (-0.25665693, -0.80901699, -0.52878982), (-0.96633118, 0.20449713, 0.15615649)-15.732, 208.188, 152.239
60generate(0.87977442, 0.10280321, -0.46414258), (-0.41527965, -0.30901699, -0.8555999), (-0.23138636, 0.945484, -0.22917317)-15.732, 208.188, 152.239

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Components

#1: Protein VP2


Mass: 61246.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Minute virus of mice / Genus: ParvovirusParvoviridae / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): prototype strain / References: UniProt: Q84367
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 30

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Sample preparation

Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 10mM Tris-HCL, 8 mM CaCl2, PEG8000 and virus 10 mgs/ml, pH 7.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12951
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSRS PX9.610.87
SYNCHROTRONEMBL/DESY, HAMBURG X3121.071
Detector
TypeIDDetector
MARRESEARCH1IMAGE PLATE
ADSC QUANTUM 42CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.871
21.0711
ReflectionResolution: 3.25→20 Å / Num. all: 557706 / Num. obs: 517599 / % possible obs: 64.2 % / Rmerge(I) obs: 0.162

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
GLRFphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: canine parvovirus model

Resolution: 3.25→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.306 -random
Rwork0.298 --
all-557706 -
obs-517599 -
Displacement parametersBiso mean: 20.86 Å2
Refinement stepCycle: LAST / Resolution: 3.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4317 0 0 121 4438
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.583

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