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- PDB-1c8g: FELINE PANLEUKOPENIA VIRUS EMPTY CAPSID STRUCTURE -

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Entry
Database: PDB / ID: 1c8g
TitleFELINE PANLEUKOPENIA VIRUS EMPTY CAPSID STRUCTURE
ComponentsFELINE PANLEUKOPENIA VIRUS CAPSID
KeywordsVIRUS / beta barrel / protein-DNA complex / double complex / 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 / T=1 icosahedral viral capsid / viral penetration into host nucleus / clathrin-dependent endocytosis of virus by host cell / host cell nucleus / virion attachment to host cell / 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 speciesFeline panleukopenia virus
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 1.3Nov 30, 2011Group: Advisory
Revision 1.4Oct 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 / cell ...atom_site / cell / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_oper_list / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_ref_seq_dif / struct_site
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[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] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: FELINE PANLEUKOPENIA VIRUS CAPSID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7013
Polymers61,6211
Non-polymers802
Water0
1
A: FELINE PANLEUKOPENIA VIRUS CAPSID
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)3,702,039180
Polymers3,697,23060
Non-polymers4,809120
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: FELINE PANLEUKOPENIA VIRUS CAPSID
hetero molecules
x 5


  • icosahedral pentamer
  • 309 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)308,50315
Polymers308,1035
Non-polymers40110
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: FELINE PANLEUKOPENIA VIRUS CAPSID
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 370 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)370,20418
Polymers369,7236
Non-polymers48112
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
Unit cell
Length a, b, c (Å)266.17, 250.12, 379.1
Angle α, β, γ (deg.)90.00, 94.11, 90.00
Int Tables number4
Space group name H-MP1211
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.45393618, 0.52041026, 0.72326696), (-0.84999798, 0.49641118, 0.17629356), (-0.26729284, -0.69480146, 0.66768663)-40.43364, 28.41263, 46.23874
3generate(-0.42961369, -0.00795643, 0.90297769), (-0.85491533, -0.31841263, -0.4095525), (0.29077809, -0.9479188, 0.12999234)-10.55875, 85.03708, 68.17822
4generate(-0.42961372, -0.85491526, 0.29077807), (-0.00795646, -0.31841262, -0.94791884), (0.90297773, -0.40955245, 0.12999236)48.33858, 91.62029, 35.49882
5generate(0.45393613, -0.84999792, -0.26729283), (0.52041028, 0.49641119, -0.69480147), (0.72326699, 0.17629358, 0.66768666)54.86425, 39.06448, -6.63764
6generate(0.17810825, -0.88967211, 0.42042944), (-0.8896722, -0.32814617, -0.31749578), (0.42042943, -0.31749574, -0.84996208)2.56037, 77.91296, 157.6973
7generate(0.72469149, -0.64106881, 0.25269147), (-0.04006647, -0.40529344, -0.91330824), (0.68790764, 0.65174225, -0.31939805)-10.47899, 89.88154, 92.37575
8generate(0.80632826, -0.11666724, 0.57984782), (0.57043173, 0.41252471, -0.71023307), (-0.15634062, 0.90344457, 0.39918101)-46.31122, 37.7559, 68.31028
9generate(0.31019932, -0.04117254, 0.94977955), (0.09813465, 0.99511138, 0.01108675), (-0.94559294, 0.08976716, 0.31272327)-55.4174, -6.42811, 118.75857
10generate(-0.078062, -0.51891582, 0.85125356), (-0.8042592, 0.53735161, 0.25381175), (-0.58912944, -0.66481544, -0.45928961)-25.21309, 18.39032, 174.00278
11generate(-0.72509807, 0.03912104, -0.68753352), (0.03912104, -0.99443272, -0.09784227), (-0.68753351, -0.09784227, 0.71953078)161.12715, 5.13777, 64.71708
12generate(-0.17862827, 0.11977094, -0.97659962), (0.88917679, -0.40530757, -0.2123451), (-0.42125603, -0.90630053, -0.03409815)159.76635, -29.22259, 123.0068
13generate(0.07814719, 0.64503851, -0.76014359), (0.80489846, 0.4090752, 0.42987909), (0.58824445, -0.64543223, -0.48722239)125.23521, -86.50967, 112.71268
14generate(-0.30962665, 0.8890218, -0.3373003), (-0.09724416, 0.3232663, 0.94129831), (0.94587258, 0.32425151, -0.01363963)105.25459, -87.55467, 48.06084
15generate(-0.80605952, 0.51454422, -0.2924248), (-0.57052064, -0.5441493, 0.61514856), (0.15739844, 0.66268072, 0.73217484)127.43703, -30.91344, 18.39792
16generate(-0.45301018, 0.85055107, 0.26710408), (0.85055115, 0.32257889, 0.41533804), (0.26710408, 0.415338, -0.8695687)53.89648, -87.67072, 168.80162
17generate(-1, 0.00088761, 0.0006412), (0.00088765, 0.31418984, 0.94935978), (0.00064123, 0.94935974, -0.31419043)108.73028, -93.69158, 129.59471
18generate(-0.45486176, -0.52041484, -0.72268192), (-0.52041485, -0.50318728, 0.68990648), (-0.72268193, 0.68990646, -0.04195096)149.21876, -40.90331, 142.01482
19generate(0.42904105, 0.00706599, -0.90325732), (0.00706598, -0.99996506, -0.00446621), (-0.90325738, -0.00446622, -0.429076)119.40822, -2.25751, 188.89778
20generate(0.43018539, 0.85436951, -0.29153593), (0.85436956, -0.4896135, -0.17415884), (-0.29153598, -0.17415886, -0.94057188)60.49581, -31.16136, 205.45293
21generate(-0.49203517, 0.5641021, 0.66309137), (-0.38165561, 0.54480637, -0.74667601), (-0.78245792, -0.62046339, -0.05277121)16.95929, 93.26269, 144.81118
22generate(-0.88007778, -0.43675041, 0.18631202), (-0.43675045, 0.59062206, -0.67853862), (0.18631203, -0.67853859, -0.71054428)83.5422, 89.64844, 156.37973
23generate(-0.07806205, -0.80425916, -0.58912941), (-0.51891587, 0.53735161, -0.66481547), (0.85125359, 0.25381176, -0.45928957)115.33256, 92.7142, 96.71272
24generate(0.80565354, -0.03053955, -0.59159923), (-0.51460206, 0.45861296, -0.72447148), (0.29344013, 0.88811117, 0.35376748)68.39717, 98.2232, 48.26793
25generate(0.54980408, 0.81515421, 0.18231577), (-0.42977054, 0.46322026, -0.77506407), (-0.71624912, 0.34777941, 0.60500964)7.59915, 98.56218, 77.99441
26generate(-0.31071835, 0.04211334, -0.94956862), (-0.86659966, 0.39783867, 0.30121332), (0.39046025, 0.91648831, -0.08712032)164.21809, 16.98419, 86.14379
27generate(0.07697034, 0.51896618, -0.85132227), (-0.81205516, -0.46277924, -0.3555304), (-0.57848253, 0.71868589, 0.3858089)134.07125, 77.25534, 92.36756
28generate(-0.17862824, 0.88917673, -0.421256), (0.11977093, -0.40530759, -0.90630056), (-0.97659966, -0.21234512, -0.03409816)106.34018, 80.50163, 154.01679
29generate(-0.72428553, 0.64112658, -0.25370678), (0.64112663, 0.49082976, -0.58995152), (-0.2537068, -0.58995153, -0.76654424)119.34827, 22.2368, 185.89433
30generate(-0.8059217, 0.11761262, -0.58022193), (0.03151609, 0.98720145, 0.1563331), (0.59118269, 0.1077059, -0.79931373)155.11878, -17.01913, 143.94651
31generate(-0.07705552, -0.64508887, 0.76021229), (0.81141591, -0.48364757, -0.32816044), (0.57936752, 0.59156178, 0.5607031)-16.50937, -13.75599, 12.13297
32generate(0.31014665, -0.88852642, 0.33812685), (0.86714543, 0.41018746, 0.28249803), (-0.38970236, 0.20558935, 0.89769987)3.42886, -75.47991, 31.44107
33generate(0.80565356, -0.51460199, 0.29344012), (-0.03053953, 0.45861298, 0.8881112), (-0.59159928, -0.72447144, 0.35376745)-18.72231, -85.8249, 94.548
34generate(0.72469151, -0.04006642, 0.68790763), (-0.64106886, -0.40529344, 0.65174225), (0.25269144, -0.9133082, -0.31939807)-52.35071, -30.49453, 114.24213
35generate(0.17914729, -0.12071175, 0.97638869), (-0.12071178, -0.98764248, -0.09995497), (0.97638872, -0.09995494, -0.1915048)-50.98304, 14.04651, 63.30685
36generate(0.87980903, 0.03887343, -0.47373504), (0.43683935, -0.45899747, 0.77362313), (-0.18736985, -0.8875867, -0.42081157)52.91599, -101.11089, 148.12806
37generate(0.49296079, 0.80631066, 0.32688339), (0.38166018, -0.53803028, 0.75157099), (0.78187286, -0.24573666, -0.57296449)-3.45831, -96.04386, 111.02764
38generate(-0.54896327, 0.42968442, 0.71694529), (0.42968447, -0.590657, 0.68300483), (0.71694534, 0.6830048, 0.13962028)14.63357, -92.01093, 45.93849
39generate(-0.80605952, -0.57052061, 0.15739838), (0.51454428, -0.54414929, 0.66268075), (-0.29242477, 0.61514856, 0.73217483)82.18927, -94.58547, 42.81161
40generate(0.07697033, -0.81205509, -0.57848254), (0.51896624, -0.46277922, 0.71868594), (-0.8513223, -0.35553037, 0.38580889)105.8491, -100.20956, 105.96824
41generate(-0.49203522, -0.38165558, -0.7824579), (0.56410213, 0.54480638, -0.62046339), (0.66309139, -0.74667596, -0.05277117)157.24745, 29.47315, 66.0333
42generate(0.31019927, 0.09813462, -0.94559291), (-0.04117253, 0.99511138, 0.08976718), (0.94977958, 0.01108675, 0.31272333)130.11851, -6.54561, 15.567
43generate(0.31014665, 0.86714535, -0.38970236), (-0.88852649, 0.41018744, 0.20558934), (0.33812689, 0.282498, 0.89769989)76.64127, 27.54359, -8.06111
44generate(-0.49212036, 0.86262991, 0.11699191), (-0.80694537, -0.40162045, -0.4330592), (-0.32658345, -0.30752333, 0.8937408)70.71944, 84.63065, 27.80222
45generate(-0.98789601, 0.0908285, -0.12574437), (0.09082849, -0.31842137, -0.94358786), (-0.12574435, -0.94358782, 0.30631737)120.5368, 85.82318, 73.59508
46generate(-0.07705551, 0.81141587, 0.57936748), (-0.64508892, -0.48364758, 0.59156177), (0.76021234, -0.32816044, 0.5607031)2.86024, -24.48046, 1.23346
47generate(-0.87954091, -0.03984994, 0.4741516), (-0.03984996, -0.98681694, -0.15685756), (0.47415167, -0.15685754, 0.86635785)55.81956, 15.2142, -12.90239
48generate(-0.49212039, -0.8069453, -0.32658347), (0.86262997, -0.40162043, -0.30752332), (0.11699194, -0.43305915, 0.89374081)112.17453, -18.46548, 3.5285
49generate(0.54980404, -0.42977049, -0.7162491), (0.81515428, 0.46322028, 0.34777946), (0.18231576, -0.77506402, 0.60500966)94.0445, -78.97533, 27.81919
50generate(0.80632825, 0.57043171, -0.15634061), (-0.11666724, 0.41252471, 0.9034446), (0.57984782, -0.71023306, 0.39918102)26.48455, -82.6928, 26.40078
51generate(0.87980905, 0.43683931, -0.18736979), (0.0388734, -0.45899748, -0.88758673), (-0.47373508, 0.77362309, -0.42081157)25.36797, 83.00983, 165.62388
52generate(0.07814723, 0.80489838, 0.58824446), (0.64503855, 0.40907519, -0.64543224), (-0.76014363, 0.42987904, -0.48722242)-6.4579, 27.35582, 187.30158
53generate(-0.80592167, 0.03151606, 0.59118267), (0.11761266, 0.98720145, 0.10770591), (-0.58022195, 0.15633307, -0.79931376)40.45129, -16.94651, 207.7224
54generate(-0.55064448, -0.81451957, -0.18261568), (-0.81451961, 0.47643045, 0.3310164), (-0.18261569, 0.3310164, -0.92578596)101.26863, 11.32716, 198.66546
55generate(0.4911944, -0.56401603, -0.66378756), (-0.86318315, -0.41736964, -0.28410828), (-0.11680318, 0.71252261, -0.69185873)91.94663, 73.10357, 172.64714
56generate(-0.31071832, -0.86659961, 0.39046021), (0.04211338, 0.39783869, 0.91648834), (-0.94956864, 0.30121331, -0.08712036)32.10834, -92.62252, 158.32536
57generate(0.49119441, -0.86318306, -0.11680316), (-0.56401606, -0.41736963, 0.71252262), (-0.66378762, -0.28410825, -0.69185875)38.10383, -40.64441, 201.2498
58generate(0.98789541, -0.09171611, 0.12510316), (-0.09171614, -0.99576847, -0.00577192), (0.12510311, -0.00577192, -0.99212694)-11.68308, 3.2484, 188.02621
59generate(0.4929608, 0.38166015, 0.78187287), (0.8063107, -0.53803028, -0.24573666), (0.32688337, 0.75157095, -0.5729645)-48.44857, -21.60247, 136.92914
60generate(-0.30962663, -0.09724418, 0.94587254), (0.88902189, 0.3232663, 0.32425154), (-0.33730029, 0.94129827, -0.01363967)-21.38398, -80.85396, 118.573

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Components

#1: Protein FELINE PANLEUKOPENIA VIRUS CAPSID


Mass: 61620.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Feline panleukopenia virus / Genus: ParvovirusParvoviridae / References: UniProt: P24840
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
Source detailsVIRUS GROWN IN A CELL CULTURE OF NORDEN LABORATORY FELINE KIDNEY CELLS

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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: 6.2
Details: 0.75-1.5% PEG8000, 8 mM CaCl2, 20 mM bis-Tris pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 7.5 / 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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.928
DetectorType: PRINCETON 2K / Detector: CCD / Date: Jan 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 584157 / Num. obs: 358402 / % possible obs: 37.4 % / Rmerge(I) obs: 0.108
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.15 / Num. unique all: 34921 / % possible all: 36.8
Reflection shell
*PLUS
% possible obs: 36.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SnBphasing
GLRFphasing
TRANSFmodel building
ENVELOPEmodel building
CNS0.5refinement
TRANSFphasing
ENVELOPEphasing
RefinementResolution: 3→9 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
Details: restrained least squares with strictly enforced icosahedral symmetry
RfactorNum. reflection% reflection
obs0.245 358402 55.3 %
Rfree-0 -
all-584157 -
Refinement stepCycle: LAST / Resolution: 3→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4350 0 2 0 4352
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.010194
X-RAY DIFFRACTIONc_angle_deg1.66476
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rwork: 0.317

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