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- PDB-4gbt: Structural characterization of H-1 Parvovirus: comparison of infe... -

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Basic information

Entry
Database: PDB / ID: 4gbt
TitleStructural characterization of H-1 Parvovirus: comparison of infectious virions to replication defective particles
ComponentsCapsid protein VP1
KeywordsVIRUS / Beta-barrel / icosahedral virus / Capsid / Capsid Proteins / Parvovirus / capsid protein
Function / homology
Function and homology information


symbiont entry into host cell via permeabilization of host membrane / microtubule-dependent intracellular transport of viral material towards nucleus / T=1 icosahedral viral capsid / viral penetration into host nucleus / host cell / 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 speciesH-1 parvovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsHalder, S. / Nam, H.-J. / Govindasamy, L. / Vogel, M. / Dinsart, C. / Salome, N. / McKenna, R. / Agbandje-McKenna, M.
CitationJournal: J.Virol. / Year: 2013
Title: Structural characterization of h-1 parvovirus: comparison of infectious virions to empty capsids.
Authors: Halder, S. / Nam, H.J. / Govindasamy, L. / Vogel, M. / Dinsart, C. / Salome, N. / McKenna, R. / Agbandje-McKenna, M.
History
DepositionJul 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4003
Polymers81,3411
Non-polymers582
Water32418
1
A: Capsid protein VP1
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)4,883,980180
Polymers4,880,47460
Non-polymers3,507120
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: Capsid protein VP1
hetero molecules
x 5


  • icosahedral pentamer
  • 407 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)406,99815
Polymers406,7065
Non-polymers29210
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP1
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 488 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)488,39818
Polymers488,0476
Non-polymers35112
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: Capsid protein VP1
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 4.88 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)4,883,980180
Polymers4,880,47460
Non-polymers3,507120
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)255.200, 350.100, 272.100
Angle α, β, γ (deg.)90.00, 90.12, 90.00
Int Tables number4
Space group name H-MP1211
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1generate(1), (1), (1)
2generate(-0.52755, 0.30578, 0.79258), (-0.71935, -0.6571, -0.22529), (0.45192, -0.689, 0.56662)43.75523, 61.27755, 0.57187
3generate(0.31668, -0.26226, 0.91155), (-0.94787, -0.05171, 0.31442), (-0.03532, -0.96361, -0.26497)-18.27773, 39.20522, 88.21573
4generate(0.36806, -0.92088, 0.12851), (-0.37153, -0.01895, 0.92823), (-0.85235, -0.38939, -0.34911)31.64978, -39.33512, 146.14355
5generate(-0.44443, -0.75988, -0.4744), (0.2132, -0.60409, 0.76787), (-0.87007, 0.24012, 0.43049)124.53958, -65.80287, 94.2997
6generate(-0.56297, -0.59766, 0.57085), (-0.6416, 0.75143, 0.15396), (-0.52097, -0.27958, -0.80649)61.08585, 30.53726, 156.04778
7generate(-0.59747, -0.64265, 0.47961), (-0.64265, 0.02601, -0.76572), (0.47962, -0.76572, -0.42853)69.49085, 93.09936, 66.42532
8generate(-0.99881, 0.02965, 0.03873), (0.02965, -0.26141, 0.96477), (0.03873, 0.96477, 0.26022)125.09649, -67.45426, 47.79525
9generate(-0.53796, -0.71496, -0.44659), (-0.71496, 0.10631, 0.69104), (-0.44659, 0.69104, -0.56835)128.62577, -1.2712, 135.11243
10generate(0.28673, -0.95563, 0.06754), (-0.95563, -0.29027, -0.05017), (0.06755, -0.05016, -0.99645)40.99056, 64.47559, 131.34926
11generate(-0.44984, 0.89299, -0.01458), (-0.72176, -0.35387, 0.59484), (0.52603, 0.27811, 0.80371)93.63848, 5.70026, -20.27584
12generate(-0.44443, 0.21321, -0.87007), (-0.75988, -0.60409, 0.24012), (-0.47441, 0.76787, 0.43049)151.42616, 32.24161, 69.01506
13generate(-0.41164, 0.90414, -0.11436), (-0.71429, -0.39802, -0.57564), (-0.56598, -0.15527, 0.80966)97.97781, 84.76153, 49.10145
14generate(-0.34578, 0.2231, -0.91141), (0.2231, -0.92392, -0.3108), (-0.91141, -0.3108, 0.2697)147.93143, 6.86374, 107.86731
15generate(0.403, -0.20112, 0.89283), (-0.27223, 0.90505, 0.32675), (-0.87378, -0.37474, 0.30998)-22.52052, -4.80812, 102.72506
16generate(-0.48491, 0.403, 0.77618), (-0.64119, 0.43974, -0.62889), (-0.59476, -0.80264, 0.04517)42.14445, 83.70904, 102.89037
17generate(-0.98838, 0.08584, -0.12541), (0.08585, -0.36561, -0.9268), (-0.12541, -0.9268, 0.35399)135.58414, 57.49357, 51.91248
18generate(-0.47173, -0.64655, 0.59954), (0.30747, 0.51665, 0.79909), (-0.8264, 0.56129, -0.04492)53.30632, -73.9489, 123.81373
19generate(-0.41164, -0.71429, -0.56598), (0.90414, -0.39802, -0.15528), (-0.11436, -0.57565, 0.80966)128.66773, -47.22452, 20.24214
20generate(-0.38995, 0.40647, 0.82627), (0.37563, 0.88947, -0.26029), (-0.84074, 0.20887, -0.49953)32.67252, -6.31573, 155.62286
21generate(-0.98333, 0.1714, -0.06065), (0.1714, 0.76261, -0.62373), (-0.06065, -0.62373, -0.77928)130.86051, 31.43148, 124.78405
22generate(-0.44984, -0.72176, 0.52603), (0.89299, -0.35387, 0.27811), (-0.01458, 0.59484, 0.80371)56.90222, -75.96239, 14.27027
23generate(-0.52755, -0.71935, 0.45191), (0.30579, -0.6571, -0.68899), (0.79258, -0.22529, 0.56662)66.90514, 27.27949, -21.19838
24generate(-0.98978, 0.13667, 0.04079), (0.13667, 0.82701, 0.54532), (0.04079, 0.54532, -0.83723)124.37862, -45.78994, 122.23875
25generate(-0.56297, -0.6416, -0.52097), (-0.59766, 0.75142, -0.27959), (0.57085, 0.15396, -0.80649)135.27925, 57.19005, 86.27811
26generate(-0.45895, 0.24917, 0.85281), (0.24917, -0.88525, 0.39274), (0.85281, 0.39274, 0.3442)35.27908, -42.61027, -9.93225
27generate(0.33555, -0.35977, 0.87062), (-0.35976, -0.90309, -0.23452), (0.87062, -0.23452, -0.43247)-16.70171, 38.92641, 41.7069
28generate(0.44228, -0.42057, -0.79215), (-0.42057, -0.87736, 0.23099), (-0.79215, 0.23099, -0.56492)89.46885, 11.17858, 156.96145
29generate(0.41652, 0.75037, 0.51328), (-0.90833, 0.36704, 0.20053), (-0.03793, -0.54975, 0.83446)2.40605, 44.4176, 13.67231
30generate(0.44828, -0.89165, 0.06333), (0.68284, 0.38729, 0.61947), (-0.57687, -0.23445, 0.78246)30.9532, -85.72932, 51.64537
31generate(-0.4849, -0.64119, -0.59476), (0.403, 0.43974, -0.80263), (0.77618, -0.62889, 0.04517)135.30434, 28.78907, 15.28437
32generate(-0.3739, 0.3114, 0.87363), (0.9259, 0.07058, 0.37112), (0.0539, 0.94765, -0.31471)28.42906, -84.38522, 85.89457
33generate(-0.38994, 0.37562, -0.84074), (0.40647, 0.88947, 0.20887), (0.82627, -0.26029, -0.49952)145.95149, -40.16758, 49.09699
34generate(0.41653, -0.90833, -0.03793), (0.75037, 0.36704, -0.54976), (0.51328, 0.20053, 0.83446)39.86284, -10.5924, -21.55083
35generate(0.47521, -0.26084, 0.84032), (0.73345, 0.645, -0.21457), (-0.48603, 0.71829, 0.49782)-23.56771, -32.28851, 65.18268
36generate(0.49882, -0.25991, -0.82681), (0.74402, 0.61771, 0.2547), (0.44453, -0.74221, 0.50151)88.21125, -64.85224, 5.46764
37generate(-0.28878, 0.95739, -0.00356), (0.95739, 0.28876, -0.00478), (-0.00355, -0.00478, -0.99998)82.59694, -60.8543, 136.13267
38generate(-0.3121, 0.32348, -0.89328), (0.94394, -0.00085, -0.33011), (-0.10755, -0.94624, -0.30508)144.54716, -37.88755, 95.55674
39generate(0.5231, -0.35159, -0.77637), (0.6084, -0.48389, 0.62905), (-0.59684, -0.8014, -0.03922)83.23181, -81.62407, 108.7575
40generate(-0.31211, 0.94394, -0.10755), (0.32348, -0.00085, -0.94623), (-0.89328, -0.33011, -0.30508)91.15392, 43.62908, 145.76666
41generate(0.9849, -0.13248, 0.11149), (-0.17274, -0.79603, 0.58008), (0.01191, -0.59058, -0.80689)-6.61091, -28.37922, 122.02347
42generate(0.5231, 0.60839, -0.59684), (-0.35159, -0.48388, -0.8014), (-0.77637, 0.62906, -0.03922)71.0322, 76.92493, 120.22992
43generate(0.59628, 0.613, -0.51834), (0.613, -0.7646, -0.19905), (-0.51834, -0.19905, -0.83168)61.02105, -25.64485, 157.59219
44generate(0.49882, 0.74402, 0.44454), (-0.25991, 0.61771, -0.74221), (-0.82682, 0.25469, 0.50151)1.81839, 67.04418, 86.70924
45generate(0.99423, -0.02572, 0.10414), (-0.09087, 0.31397, 0.94507), (-0.057, -0.94908, 0.30982)-6.70753, -58.41454, 50.54273
46generate(0.47522, 0.73345, -0.48603), (-0.26084, 0.64499, 0.71829), (0.84032, -0.21457, 0.49782)66.56185, -32.14222, -19.57317
47generate(0.52634, 0.62911, 0.572), (0.62911, -0.7407, 0.23576), (0.572, 0.23576, -0.78564)-8.60164, -56.22236, 84.78798
48generate(0.99423, -0.09086, -0.057), (-0.02572, 0.31398, -0.94908), (0.10413, 0.94507, 0.30983)4.24236, 66.13664, 40.24473
49generate(0.56669, 0.66908, 0.48082), (0.69028, -0.06692, -0.72044), (-0.44986, 0.74017, -0.49978)-4.98396, 4.84557, 130.6611
50generate(-0.99795, -0.00176, -0.06399), (-0.00176, -0.99849, 0.05495), (-0.06399, 0.05495, 0.99644)132.02119, -3.62133, 4.33115
51generate(0.56669, 0.69028, -0.44986), (0.66908, -0.06691, 0.74017), (0.48083, -0.72044, -0.49977)58.2589, -93.05258, 71.18925
52generate(0.43353, -0.35889, 0.82659), (0.67935, -0.4725, -0.56146), (0.59206, 0.80495, 0.03897)-19.97068, -5.25851, 27.47092
53generate(0.403, -0.27223, -0.87377), (-0.20112, 0.90505, -0.37474), (0.89283, 0.32676, 0.30999)97.52573, 38.31606, -10.16499
54generate(-0.37391, 0.9259, 0.0539), (0.3114, 0.07058, 0.94766), (0.87363, 0.37112, -0.31471)84.13155, -84.2953, 33.51218
55generate(-0.47173, 0.30747, -0.8264), (-0.64655, 0.51665, 0.56129), (0.59954, 0.79909, -0.04492)150.20272, 3.1739, 32.69391
56generate(0.31668, -0.94787, -0.03532), (-0.26226, -0.05171, -0.96361), (0.91155, 0.31442, -0.26497)46.06545, 82.23957, 27.70836
57generate(0.9849, -0.17274, 0.01191), (-0.13247, -0.79603, -0.59058), (0.1115, 0.58008, -0.80689)0.15599, 48.59755, 115.65965
58generate(0.44828, 0.68284, -0.57687), (-0.89165, 0.38729, -0.23445), (0.06332, 0.61947, 0.78247)74.45648, 72.90991, 10.735
59generate(0.43353, 0.67935, 0.59206), (-0.35889, -0.4725, 0.80495), (0.82659, -0.56145, 0.03897)-4.03448, -31.7654, 12.48457
60generate(0.36806, -0.37153, -0.85235), (-0.92088, -0.01895, -0.38939), (0.12851, 0.92823, -0.34911)98.30245, 85.30582, 83.46339
DetailsT=1 symmetry

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Components

#1: Protein Capsid protein VP1 / Coat protein VP1


Mass: 81341.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Infection in NB324K cells / Source: (natural) H-1 parvovirus / References: UniProt: P03136
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS HAVE DEPOSITED THE CORRECT SEQUENCE IN THE GENBANK DATABASE ACCESSION CODE JX505432.1

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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: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10 mM Tris-HCl, 150 mM NaCl, 8mM CaCl2.2H2O and 3% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0895 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2008 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0895 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. all: 782183 / Num. obs: 479478 / % possible obs: 61.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Rsym value: 0.114 / Net I/σ(I): 4.9
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.4 / % possible all: 58.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.3refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementResolution: 3.2→40 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2592 22657 2.9 %
Rwork0.2563 433649 -
obs-456306 58.4 %
Solvent computationBsol: 10.7716 Å2
Displacement parametersBiso max: 128.24 Å2 / Biso mean: 61.7723 Å2 / Biso min: 16.7 Å2
Baniso -1Baniso -2Baniso -3
1-6.771 Å20 Å2-1.744 Å2
2---16.134 Å20 Å2
3---9.363 Å2
Refinement stepCycle: LAST / Resolution: 3.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4366 0 2 18 4386
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.366
X-RAY DIFFRACTIONc_mcbond_it1.1861.5
X-RAY DIFFRACTIONc_scbond_it1.612
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scangle_it2.7062.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.310.387419390.3821366813862049.5
3.31-3.450.351319950.3481384304042551.8
3.45-3.60.318321000.3196400244212454
3.6-3.790.301822310.295421434437456.9
3.79-4.030.276323170.2758438404615759.1
4.03-4.340.248123390.2472451734751260.8
4.34-4.780.231324010.2296459584835961.8
4.78-5.470.233124350.2218477825021764.2
5.47-6.880.223225090.2195479955050464.5
6.88-400.210323910.2123456234801461

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