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- PDB-1c8d: CANINE PANLEUKOPENIA VIRUS EMPTY CAPSID STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1c8d
TitleCANINE PANLEUKOPENIA VIRUS EMPTY CAPSID STRUCTURE
ComponentsCANINE PARVOVIRUS CAPSID
KeywordsVIRUS / Capsid / canine parvovirus / strain D / empty capsid / A300D / 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 / 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
Capsid protein VP1 / Capsid protein VP1
Similarity search - Component
Biological speciesCanine parvovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsRossmann, M.G. / Simpson, A.A.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Host range and variability of calcium binding by surface loops in the capsids of canine and feline parvoviruses.
Authors: Simpson, A.A. / Chandrasekar, V. / Hebert, B. / Sullivan, G.M. / Rossmann, M.G. / Parrish, C.R.
#1: Journal: Protein Sci. / Year: 1993
Title: Structure Determination of Feline Panleukopenia Virus Empty Particles
Authors: Agbandje, M. / McKenna, R. / Rossmann, M.G. / Strassheim, M.L. / Parrish, C.R.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structural Refinement of the DNA-Containing Capsid of Canine Parvovirus using RSRef, a Resolution-Dependent Stereochemically Restrained Real-Space Refinement Method
Authors: Chapman, M.S. / Rossmann, M.G.
#3: Journal: VIROLOGY / Year: 1996
Title: Structural Analysis of a Mutation in Canine Parvovirus which Controls Antigenicity and Host Range
Authors: Llamas-Saiz, A.L. / Agbandje-McKenna, M. / Parker, J.S. / Wahid, A.T. / Parrish, C.R. / Rossmann, M.G.
#4: 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.
History
DepositionMay 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / atom_sites ...atom_site / atom_sites / cell / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][2] / _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[1][3] / _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] / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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[3] / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CANINE PARVOVIRUS CAPSID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8242
Polymers64,7841
Non-polymers401
Water0
1
A: CANINE PARVOVIRUS CAPSID
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)3,889,422120
Polymers3,887,01860
Non-polymers2,40560
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: CANINE PARVOVIRUS CAPSID
hetero molecules
x 5


  • icosahedral pentamer
  • 324 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)324,11910
Polymers323,9185
Non-polymers2005
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: CANINE PARVOVIRUS CAPSID
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 389 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)388,94212
Polymers388,7026
Non-polymers2406
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: CANINE PARVOVIRUS CAPSID
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 3.89 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)3,889,422120
Polymers3,887,01860
Non-polymers2,40560
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)267.563, 268.446, 274.328
Angle α, β, γ (deg.)61.946, 62.616, 60.186
Int Tables number1
Space group name H-MP1
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.58638074, -0.78992652, 0.17937028), (0.64996475, 0.32667368, -0.68617062), (0.48342882, 0.51894161, 0.70497956)
3generate(-0.08286926, -0.6281632, 0.77365604), (0.26173854, -0.76279119, -0.59130578), (0.96157454, 0.15349455, 0.22762647)
4generate(-0.08286926, 0.26173855, 0.96157454), (-0.62816321, -0.76279119, 0.15349453), (0.77365604, -0.59130576, 0.22762647)
5generate(0.58638074, 0.64996476, 0.48342882), (-0.78992653, 0.32667368, 0.5189416), (0.17937029, -0.68617061, 0.70497955)
6generate(-0.65639867, 0.27578595, 0.70219861), (0.27578595, -0.77864495, 0.56360815), (0.70219861, 0.56360817, 0.43504362)
7generate(0.13381465, 0.97299881, 0.18806104), (-0.07191179, -0.17973372, 0.98108331), (0.98839381, -0.14480711, 0.04591906)
8generate(0.80179539, 0.30974205, -0.51106163), (0.31529567, 0.50721571, 0.80207285), (0.50765417, -0.80423385, 0.30902288)
9generate(0.42441688, -0.79738602, -0.42900563), (0.90230079, 0.33286258, 0.27396313), (-0.07565446, -0.50336669, 0.86075452)
10generate(-0.47679662, -0.81837204, 0.32083043), (0.87788242, -0.46184301, 0.12658384), (0.0445806, 0.34200616, 0.93863963)
11generate(-0.4287139, -0.90039759, 0.07408493), (-0.90039759, 0.41910649, -0.11676443), (0.07408494, -0.11676444, -0.99039259)
12generate(-0.80080148, 0.08296204, 0.5931562), (-0.31201864, 0.78756507, -0.53139966), (-0.51123511, -0.61062146, -0.60479757)
13generate(-0.12890337, 0.96748927, 0.21759689), (0.0720339, 0.22798318, -0.9709968), (-0.98903742, -0.10949041, -0.09907982)
14generate(0.6584401, 0.53079754, -0.53358278), (-0.27898751, -0.48631603, -0.82804752), (-0.69901545, 0.69408262, -0.17212407)
15generate(0.473147, -0.62362002, -0.62227806), (-0.87998321, -0.36819532, -0.30010288), (-0.04196969, 0.68958702, -0.72298566)
16generate(0.08511257, 0.62461163, -0.77628354), (0.62461164, -0.64046154, -0.44684372), (-0.77628355, -0.44684372, -0.44465103)
17generate(0.08060608, -0.26603433, -0.96058752), (-0.26603433, -0.93450503, 0.23648697), (-0.96058751, 0.23648696, -0.14610106)
18generate(-0.59002277, -0.64906813, -0.4801913), (-0.64906812, 0.0275923, 0.76022972), (-0.48019129, 0.76022971, -0.43756953)
19generate(-0.99998772, 0.00484992, 0.00101387), (0.00484993, 0.91624464, 0.40058985), (0.00101387, 0.40058983, -0.91625691)
20generate(-0.58273113, 0.7920273, -0.18198119), (0.79202732, 0.50336466, -0.34542256), (-0.1819812, -0.34542257, -0.92063352)
21generate(-0.4774516, -0.82079782, -0.3135776), (0.6225258, -0.06413993, -0.77996647), (0.62008192, -0.56760638, 0.54159154)
22generate(-0.96505053, -0.05370983, 0.25650091), (-0.05370983, -0.91745953, -0.39418685), (0.25650091, -0.39418683, 0.88251005)
23generate(-0.47679661, 0.87788242, 0.04458061), (-0.81837205, -0.46184302, 0.34200615), (0.32083044, 0.12658386, 0.93863962)
24generate(0.31255984, 0.6865501, -0.65647184), (-0.61472368, 0.67306305, 0.41121883), (0.72416929, 0.2750183, 0.63241108)
25generate(0.31215504, -0.36329202, -0.8778258), (0.27580017, 0.91885707, -0.28219838), (0.90911687, -0.15401487, 0.38702186)
26generate(-0.13315967, 0.33070073, -0.93429413), (-0.97400538, -0.21796937, 0.06166753), (-0.18325398, 0.91821914, 0.35112902)
27generate(-0.31480315, -0.27162652, -0.90946028), (-0.68299854, 0.73018967, 0.0183309), (0.65909936, 0.62693066, -0.41538652)
28generate(-0.80080148, -0.31201866, -0.51123511), (0.08296205, 0.78756507, -0.61062144), (0.59315619, -0.53139967, -0.60479757)
29generate(-0.91952149, 0.26534488, -0.28995226), (0.26534489, -0.12513402, -0.95599872), (-0.28995227, -0.95599872, 0.04465551)
30generate(-0.50689615, 0.6625673, -0.55141711), (-0.3878969, -0.74658847, -0.5405013), (-0.76980015, -0.06008502, 0.63545064)
31generate(0.92050313, 0.12250929, 0.37103295), (-0.26691779, -0.49632985, 0.82608206), (0.28535746, -0.85944642, -0.42417329)
32generate(0.79876005, -0.49456483, 0.34261928), (-0.07976048, 0.4773959, 0.87506081), (-0.59633935, -0.72629112, 0.34187803)
33generate(0.31255984, -0.61472366, 0.72416928), (0.68655011, 0.67306306, 0.27501829), (-0.65647185, 0.41121881, 0.63241108)
34generate(0.13381465, -0.07191177, 0.9883938), (0.97299881, -0.17973372, -0.14480713), (0.18806103, 0.98108331, 0.04591908)
35generate(0.50954426, 0.38372325, 0.77014356), (0.38372323, -0.90245828, 0.195769), (0.77014356, 0.19576901, -0.60708597)
36generate(-0.30989187, 0.3675878, 0.87683878), (0.61839736, 0.77843915, -0.10778312), (-0.72218539, 0.50883366, -0.46854727)
37generate(0.48109362, 0.81990119, 0.31034008), (0.81646885, -0.29012604, -0.49920485), (-0.31926091, 0.49354728, -0.80900156)
38generate(0.96503825, 0.04885991, -0.25751478), (0.04885989, -0.99878511, -0.006403), (-0.25751478, -0.006403, -0.96625314)
39generate(0.473147, -0.8799832, -0.0419697), (-0.62362002, -0.36819531, 0.68958703), (-0.62227805, -0.30010289, -0.72298566)
40generate(-0.31480315, -0.68299853, 0.65909935), (-0.27162651, 0.73018968, 0.62693067), (-0.90946028, 0.01833088, -0.41538652)
41generate(-0.47745159, 0.6225258, 0.62008193), (-0.82079781, -0.06413995, -0.56760639), (-0.3135776, -0.77996646, 0.54159154)
42generate(0.42441689, 0.90230078, -0.07565445), (-0.79738602, 0.33286255, -0.5033667), (-0.42900562, 0.27396314, 0.86075453)
43generate(0.79876005, -0.07976048, -0.59633935), (-0.49456485, 0.47739588, -0.72629111), (0.34261929, 0.87506081, 0.34187804)
44generate(0.12824838, -0.96648271, -0.22240393), (-0.33082286, 0.16971988, -0.92830565), (0.93493775, 0.19263, -0.29796826)
45generate(-0.6604938, -0.53244591, 0.52938576), (-0.53244591, -0.16496766, -0.83023311), (0.52938576, -0.8302331, -0.17453854)
46generate(0.92050313, -0.26691777, 0.28535746), (0.12250928, -0.49632986, -0.85944642), (0.37103296, 0.82608206, -0.42417327)
47generate(0.50422818, -0.66624099, 0.54943321), (-0.666241, -0.70491374, -0.24335067), (0.54943323, -0.24335067, -0.79931443)
48generate(0.12824838, -0.33082285, 0.93493774), (-0.96648271, 0.16971989, 0.19263), (-0.22240393, -0.92830566, -0.29796827)
49generate(0.31215504, 0.27580018, 0.90911687), (-0.36329201, 0.91885707, -0.15401487), (-0.8778258, -0.28219839, 0.38702187)
50generate(0.80179539, 0.31529569, 0.50765418), (0.30974206, 0.50721569, -0.80423385), (-0.51106163, 0.80207285, 0.3090229)
51generate(-0.30989186, 0.61839735, -0.72218539), (0.36758779, 0.77843915, 0.50883368), (0.87683877, -0.10778312, -0.46854729)
52generate(-0.12890337, 0.07203389, -0.98903742), (0.96748928, 0.2279832, -0.1094904), (0.21759688, -0.97099679, -0.09907983)
53generate(-0.50689615, -0.38789691, -0.76980015), (0.66256732, -0.74658846, -0.06008503), (-0.55141712, -0.54050129, 0.63545063)
54generate(-0.92149705, -0.12578632, -0.36745202), (-0.12578631, -0.79845091, 0.58877323), (-0.36745202, 0.58877324, 0.71994796)
55generate(-0.79974169, 0.49613773, -0.33802448), (-0.30809369, 0.14406798, 0.94038433), (0.51525866, 0.85620777, 0.03763973)
56generate(-0.13315967, -0.97400538, -0.183254), (0.33070074, -0.21796934, 0.91821913), (-0.93429413, 0.06166752, 0.35112902)
57generate(-0.7997417, -0.30809369, 0.51525866), (0.49613775, 0.14406798, 0.85620777), (-0.33802448, 0.94038433, 0.03763974)
58generate(-0.42011229, 0.79848024, 0.43120176), (0.79848024, 0.09947269, 0.59374614), (0.43120175, 0.59374614, -0.6793604)
59generate(0.48109363, 0.81646885, -0.31926091), (0.81990118, -0.29012603, 0.49354729), (0.31034008, -0.49920485, -0.80900157)
60generate(0.65844009, -0.27898751, -0.69901546), (0.53079754, -0.486316, 0.69408262), (-0.53358279, -0.82804752, -0.17212409)

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Components

#1: Protein CANINE PARVOVIRUS CAPSID / CPV


Mass: 64783.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CAPSID OF CANINE PARVOVIRUS STRAIN D - EMPTY CAPSID
Source: (natural) Canine parvovirus / Genus: ParvovirusParvoviridae / Species: Feline panleukopenia virus / Strain: D / References: UniProt: P30129, UniProt: P17455*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Source detailsVIRUS GROWN IN A CELL CULTURE OF NORDEN LABORATORY FELINE KIDNEY CELL

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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: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.75-1.5% PEG8000, 20 mM TRIS pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlvirus1drop
220 mMBis-Tris1drop
320 mMTris-HCl1drop
40.75-1.50 %PEG80001reservoir
58 mM1reservoiror 5mM EDTACaCl2

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jan 15, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 1031521 / Num. obs: 322866 / % possible obs: 31.3 % / Rmerge(I) obs: 0.09

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Processing

Software
NameVersionClassification
GLRFphasing
ENVELOPEmodel building
CNS0.5refinement
ENVELOPEphasing
RefinementResolution: 3→9 Å / Stereochemistry target values: Engh & Huber
Details: restrained least squares with strictly enforced icosahedral symmetry
RfactorNum. reflection% reflection
obs0.214 322866 31.3 %
Rfree-0 -
all-1031521 -
Refinement stepCycle: LAST / Resolution: 3→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4352 0 1 0 4353
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.588
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rwork: 0.281

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