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- PDB-2cas: THE CANINE PARVOVIRUS EMPTY CAPSID STRUCTURE -

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Entry
Database: PDB / ID: 2cas
TitleTHE CANINE PARVOVIRUS EMPTY CAPSID STRUCTURE
ComponentsCANINE PARVOVIRUS EMPTY CAPSID (STRAIN D) VIRAL PROTEIN 2
KeywordsVIRUS / PARVOVIRUS COAT PROTEIN / 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 / adhesion receptor-mediated virion attachment to host cell / T=1 icosahedral viral capsid / host cell / viral penetration into host nucleus / clathrin-dependent endocytosis of virus by host cell / entry receptor-mediated virion attachment to host cell / host cell nucleus ...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 / adhesion receptor-mediated virion attachment to host cell / T=1 icosahedral viral capsid / host cell / viral penetration into host nucleus / clathrin-dependent endocytosis of virus by host cell / entry receptor-mediated virion attachment to host cell / host cell nucleus / 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 speciesCanine parvovirus
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsWu, H. / Rossmann, M.G.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: The canine parvovirus empty capsid structure.
Authors: Wu, H. / Rossmann, M.G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Determination and Refinement of the Canine Parvovirus Empty Capsid Structure
Authors: Wu, H. / Keller, W. / Rossmann, M.G.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1992
Title: Structure Determination of Monoclinic Canine Parvovirus
Authors: Tsao, J. / Chapman, M.S. / Wu, H. / Agbandje, M. / Keller, W. / Rossmann, M.G.
#3: 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.
#4: Journal: J.Mol.Biol. / Year: 1988
Title: Preliminary X-Ray Crystallographic Analysis of Canine Parvovirus Crystals
Authors: Luo, M. / Tsao, J. / Rossmann, M.G. / Basak, S. / Compans, R.W.
History
DepositionAug 24, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 7, 2011Group: Structure summary
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_database_status / pdbx_struct_oper_list / 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[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _pdbx_database_status.process_site / _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_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
Remark 700SHEET THE STRUCTURE OF CANINE PARVOVIRUS FOLLOWS THE CANONICAL PICORNA-VIRUS LIKE "JELLY ROLL" ...SHEET THE STRUCTURE OF CANINE PARVOVIRUS FOLLOWS THE CANONICAL PICORNA-VIRUS LIKE "JELLY ROLL" BARREL. THE SHEET IDENTIFIED AS "BDG" IS THAT REFERRED TO AS "BIDG" IN THE LITERATURE WITH STRANDS 1 TO 5 CORRESPONDING TO STRANDS A, B, I, D, AND G. THE SHEET IDENTIFIED AS "CHF" IS THE SO-CALLED CHEF SHEET WITH STRANDS 1 TO 4 CORRESPONDING TO STRANDS C, H, E, AND F. THESE TWO SHEETS ARE LOOSELY CONNECTED TOGETHER BY HYDROGEN BONDS BETWEEN STRAND 4 OF "CHF" AND RESIDUE 45 IMMEDIATELY PRECEDING STRAND 1 OF "BDG" OF A FIVE-FOLD RELATED PROTOMER THAT IS NOT EXPLICITLY PRESENTED ON THE ATOM RECORDS, BUT WHICH CAN BE GENERATED USING THE SYMMETRY OPERATORS LISTED BELOW. CPV CONTAINS SEVERAL LONG LOOPS BETWEEN STRANDS OF "BDG" AND "CHF" WITH ONLY A FEW ORGANIZED SECONDARY STRUCTURES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CANINE PARVOVIRUS EMPTY CAPSID (STRAIN D) VIRAL PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)61,5621
Polymers61,5621
Non-polymers00
Water1,56787
1
A: CANINE PARVOVIRUS EMPTY CAPSID (STRAIN D) VIRAL PROTEIN 2
x 60


Theoretical massNumber of molelcules
Total (without water)3,693,74260
Polymers3,693,74260
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: CANINE PARVOVIRUS EMPTY CAPSID (STRAIN D) VIRAL PROTEIN 2
x 5


  • icosahedral pentamer
  • 308 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)307,8125
Polymers307,8125
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: CANINE PARVOVIRUS EMPTY CAPSID (STRAIN D) VIRAL PROTEIN 2
x 6


  • icosahedral 23 hexamer
  • 369 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)369,3746
Polymers369,3746
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: CANINE PARVOVIRUS EMPTY CAPSID (STRAIN D) VIRAL PROTEIN 2
x 30


  • crystal asymmetric unit, crystal frame
  • 1.85 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)1,846,87130
Polymers1,846,87130
Non-polymers00
Water54030
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)254.500, 254.500, 795.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: ELECTRON DENSITY FOR RESIDUES 155 - 163 AND 361 - 372 IS WEAK.
2: CIS PROLINE - PRO 465
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.48631532, -0.70550442, 0.51552076), (0.87137665, 0.34781245, -0.34601837), (0.06481287, 0.61748693, 0.78390622)165.47426, -29.74941, -92.60504
3generate(-0.3448451, -0.2701535, 0.89894306), (0.70441302, -0.7074484, 0.05761731), (0.62039041, 0.65309571, 0.43425952)219.19544, 136.13683, -172.84371
4generate(-0.34484582, 0.7044126, 0.62039032), (-0.27015283, -0.70744792, 0.65309624), (0.89894333, 0.05761622, 0.43425976)86.9227, 268.40957, -129.8289
5generate(0.48631416, 0.87137664, 0.06481295), (-0.70550402, 0.34781322, 0.61748679), (0.51552097, -0.34601913, 0.78390661)-48.54753, 184.27238, -23.00561
6generate(-0.94977884, -0.05022116, 0.30886529), (-0.05022116, -0.94977884, -0.30886529), (0.30886605, -0.30886605, 0.89955767)271.4497, 271.4497
7generate(-0.4856351, 0.8433259, -0.23013184), (-0.87205687, -0.48563392, 0.06062945), (-0.06062945, 0.23013129, 0.97126903)87.17732, 319.99723, -23.00561
8generate(0.4837672, 0.49383355, -0.72256301), (-0.84333512, 0.48376835, -0.23399736), (0.23399674, 0.7225628, 0.65049844)3.04013, 184.527, -129.8289
9generate(0.61874704, -0.61571167, -0.48790508), (-0.00374839, 0.61874699, -0.78558148), (0.78558123, 0.48790489, 0.38053995)135.31287, 52.25426, -172.84371
10generate(-0.26723313, -0.95195597, 0.14955267), (0.48642299, -0.26723389, -0.83185241), (0.83185301, -0.1495532, 0.53446701)301.19911, 105.97544, -92.60504
11generate(0.70853412, -0.48443366, 0.51313174), (0.26603246, -0.49013291, -0.83005793), (0.65361021, 0.72463381, -0.2184012)105.30885, 166.14085, -187.06196
12generate(-0.04429564, -0.35151386, 0.93513415), (-0.35151315, -0.87071132, -0.34394732), (0.93513444, -0.34394812, -0.08499304)189.44604, 301.61108, -80.23867
13generate(-0.26723389, 0.48642299, 0.83185241), (-0.95195597, -0.26723313, -0.14955267), (0.1495532, -0.83185301, 0.53446701)105.97544, 301.19911, 92.60504
14generate(0.34781245, 0.87137665, 0.34601837), (-0.70550442, 0.48631532, -0.51552076), (-0.61748693, -0.06481287, 0.78390622)-29.74941, 165.47426, 92.60504
15generate(0.95087023, 0.27135424, 0.14903816), (0.04725382, 0.34855568, -0.93609614), (-0.30596257, 0.89714889, 0.31860807)-30.16138, 82.00366, -80.23867
16generate(-0.49013291, 0.26603246, 0.83005793), (-0.48443366, 0.70853412, -0.51313174), (-0.72463381, -0.65361021, -0.2184012)166.14085, 105.30885, 187.06196
17generate(0.04725376, 0.95087026, 0.30596176), (0.34855503, 0.27135493, -0.89714859), (-0.93609641, 0.14903871, -0.3186087)0.25462, 51.58766, 106.82329
18generate(0.87137664, 0.48631416, -0.06481295), (0.34781322, -0.70550402, -0.61748679), (-0.34601913, 0.51552097, -0.78390661)-48.54753, 184.27238, -23.00561
19generate(0.8433259, -0.4856351, 0.23013184), (-0.48563392, -0.87205687, -0.06062945), (0.23013129, -0.06062945, -0.97126903)87.17732, 319.99723, -23.00561
20generate(0.00186673, -0.62177668, 0.78319246), (-0.99999078, 0.00186676, 0.00386552), (-0.00386545, -0.78319226, -0.62176747)219.86204, 271.19508, 106.82329
21generate(0.70853366, 0.26603172, 0.65361075), (-0.48443253, -0.49013285, 0.72463406), (0.51313199, -0.83005857, -0.21840082)3.45211, 267.99759, 43.01481
22generate(0.61874699, -0.00374839, 0.78558148), (-0.61571167, 0.61874704, 0.48790508), (-0.48790489, -0.78558123, 0.38053995)52.25426, 135.31287, 172.84371
23generate(0.34855568, 0.04725382, 0.93609614), (0.27135424, 0.95087023, -0.14903816), (-0.89714889, 0.30596257, 0.31860807)82.00366, -30.16138, 80.23867
24generate(0.27135493, 0.34855503, 0.89714859), (0.95087026, 0.04725376, -0.30596176), (-0.14903871, 0.93609641, -0.3186087)51.58766, 0.25462, -106.82329
25generate(0.49383355, 0.4837672, 0.72256301), (0.48376835, -0.84333512, 0.23399736), (0.7225628, 0.23399674, -0.65049844)3.04013, 184.527, -129.8289
26generate(0.26603172, 0.70853366, -0.65361075), (-0.49013285, -0.48443253, -0.72463406), (-0.83005857, 0.51313199, 0.21840082)3.45211, 267.99759, 43.01481
27generate(0.7044126, -0.34484582, -0.62039032), (-0.70744792, -0.27015283, -0.65309624), (0.05761622, 0.89894333, -0.43425976)86.9227, 268.40957, -129.8289
28generate(0.00186676, -0.99999078, -0.00386552), (-0.62177668, 0.00186673, -0.78319246), (0.78319226, 0.00386545, -0.62176747)271.19508, 219.86204, -106.82329
29generate(-0.87071132, -0.35151315, 0.34394732), (-0.35151386, -0.04429564, -0.93513415), (0.34394812, -0.93513444, -0.08499304)301.61108, 189.44604, 80.23867
30generate(-0.7074484, 0.70441302, -0.05761731), (-0.2701535, -0.3448451, -0.89894306), (-0.65309571, -0.62039041, 0.43425952)136.13683, 219.19544, 172.84371

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Components

#1: Protein CANINE PARVOVIRUS EMPTY CAPSID (STRAIN D) VIRAL PROTEIN 2


Mass: 61562.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canine parvovirus / Genus: ParvovirusParvoviridae / Species: Feline panleukopenia virus / Strain: D / References: UniProt: Q11213
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 200.209-211 1988
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.75 %PEG80001reservoir
26 mM1reservoirCaCl2
310 mMTris-HCl1reservoir
410 mg/mlvirus1drop
50.75 %PEG80001drop
66 mM1dropCaCl2
710 mMTris-HCl1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor obs: 0.211 / Highest resolution: 3 Å
Details: ELECTRON DENSITY FOR RESIDUES 155 - 163 AND 361 - 372 IS WEAK.
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4347 0 0 87 4434
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d2.9
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 3 Å / Rfactor obs: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS

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