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- PDB-4qc8: Structural annotation of pathogenic bovine Parvovirus-1 -

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Basic information

Entry
Database: PDB / ID: 4qc8
TitleStructural annotation of pathogenic bovine Parvovirus-1
ComponentsVP2
KeywordsVIRUS / parvovirus / capsid protein / beta barrel / VP2 / ssDNA virus / jellyroll / nucleoplasmin-like/VP / viral coat / coat protein
Function / homology
Function and homology information


T=1 icosahedral viral capsid / 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
Capsid protein VP2 / VP2
Similarity search - Component
Biological speciesBovine parvovirus-1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKailasan, S. / Halder, S. / Gurda, B.L. / Bladek, H. / Chipman, P.R. / McKenna, R. / Brown, K. / Agbandje-McKenna, M.
CitationJournal: J Virol / Year: 2015
Title: Structure of an enteric pathogen, bovine parvovirus.
Authors: Shweta Kailasan / Sujata Halder / Brittney Gurda / Heather Bladek / Paul R Chipman / Robert McKenna / Kevin Brown / Mavis Agbandje-McKenna /
Abstract: Bovine parvovirus (BPV), the causative agent of respiratory and gastrointestinal disease in cows, is the type member of the Bocaparvovirus genus of the Parvoviridae family. Toward efforts to obtain a ...Bovine parvovirus (BPV), the causative agent of respiratory and gastrointestinal disease in cows, is the type member of the Bocaparvovirus genus of the Parvoviridae family. Toward efforts to obtain a template for the development of vaccines and small-molecule inhibitors for this pathogen, the structure of the BPV capsid, assembled from the major capsid viral protein 2 (VP2), was determined using X-ray crystallography as well as cryo-electron microscopy and three-dimensional image reconstruction (cryo-reconstruction) to 3.2- and 8.8-Å resolutions, respectively. The VP2 region ordered in the crystal structure, from residues 39 to 536, conserves the parvoviral eight-stranded jellyroll motif and an αA helix. The BPV capsid displays common parvovirus features: a channel at and depressions surrounding the 5-fold axes and protrusions surrounding the 3-fold axes. However, rather than a depression centered at the 2-fold axes, a raised surface loop divides this feature in BPV. Additional observed density in the capsid interior in the cryo-reconstructed map, compared to the crystal structure, is interpreted as 10 additional N-terminal residues, residues 29 to 38, that radially extend the channel under the 5-fold axis, as observed for human bocavirus 1 (HBoV1). Surface loops of various lengths and conformations extend from the core jellyroll motif of VP2. These loops confer the unique surface topology of the BPV capsid, making it strikingly different from HBoV1 as well as the type members of other Parvovirinae genera for which structures have been determined. For the type members, regions structurally analogous to those decorating the BPV capsid surface serve as determinants of receptor recognition, tissue and host tropism, pathogenicity, and antigenicity.
IMPORTANCE: Bovine parvovirus (BPV), identified in the 1960s in diarrheic calves, is the type member of the Bocaparvovirus genus of the nonenveloped, single-stranded DNA (ssDNA) Parvoviridae family. ...IMPORTANCE: Bovine parvovirus (BPV), identified in the 1960s in diarrheic calves, is the type member of the Bocaparvovirus genus of the nonenveloped, single-stranded DNA (ssDNA) Parvoviridae family. The recent isolation of human bocaparvoviruses from children with severe respiratory and gastrointestinal infections has generated interest in understanding the life cycle and pathogenesis of these emerging viruses. We have determined the high-resolution structure of the BPV capsid assembled from its predominant capsid protein VP2, known to be involved in a myriad of functions during host cell entry, pathogenesis, and antigenicity for other members of the Parvovirinae. Our results show the conservation of the core secondary structural elements and the location of the N-terminal residues for the known bocaparvovirus capsid structures. However, surface loops with high variability in sequence and conformation give BPV a unique capsid surface topology. Similar analogous regions in other Parvovirinae type members are important as determinants of receptor recognition, tissue and host tropism, pathogenicity, and antigenicity.
History
DepositionMay 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _software.name
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP2


Theoretical massNumber of molelcules
Total (without water)59,7431
Polymers59,7431
Non-polymers00
Water00
1
A: VP2
x 60


Theoretical massNumber of molelcules
Total (without water)3,584,59860
Polymers3,584,59860
Non-polymers00
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: VP2
x 5


  • icosahedral pentamer
  • 299 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)298,7165
Polymers298,7165
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP2
x 6


  • icosahedral 23 hexamer
  • 358 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)358,4606
Polymers358,4606
Non-polymers00
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: VP2
x 30


  • crystal asymmetric unit, crystal frame
  • 1.79 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)1,792,29930
Polymers1,792,29930
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)323.450, 381.230, 376.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1generate(1), (1), (1)
2generate(0.49909, -0.80933, -0.30968), (0.81018, 0.30902, 0.49812), (-0.30745, -0.4995, 0.80992)-105.56285, -18.13843, -65.0515
3generate(-0.3114, -0.49934, -0.80851), (0.50156, -0.80902, 0.30648), (-0.80714, -0.31008, 0.50237)-123.423, -141.67214, -76.22373
4generate(-0.31139, 0.50156, -0.80714), (-0.49934, -0.80902, -0.31009), (-0.80852, 0.30647, 0.50237)-28.89909, -199.88018, -18.07741
5generate(0.4991, 0.81017, -0.30745), (-0.80932, 0.30902, -0.4995), (-0.30968, 0.49812, 0.80992)47.38035, -112.32287, 29.03288
6generate(0.59764, 0.00237, -0.80176), (0.00237, -1, -0.00119), (-0.80176, -0.00119, -0.59765)-75.11661, -188.72901, -150.24097
7generate(0.54465, 0.08555, -0.83429), (0.81087, -0.30769, 0.49781), (-0.21411, -0.94763, -0.23695)-70.34365, -76.32879, -205.44636
8generate(0.99461, -0.08327, 0.06184), (0.08477, 0.30902, -0.94727), (0.05977, 0.9474, 0.31441)-2.05753, -153.96011, 25.08335
9generate(0.54465, 0.81087, -0.21411), (0.08556, -0.30769, -0.94763), (-0.83429, 0.49781, -0.23696)56.21647, -212.1548, -69.37071
10generate(-0.31812, 0.58518, -0.7459), (0.58518, -0.4978, -0.64012), (-0.7459, -0.64012, -0.18407)-15.27355, -201.05275, -171.69478
11generate(0.40929, -0.58505, 0.70015), (0.86178, 0.49995, -0.08601), (-0.29971, 0.63857, 0.7088)10.24613, -54.88714, 32.79949
12generate(0.46095, 0.49956, 0.73346), (0.05212, 0.80984, -0.58434), (-0.8859, 0.30758, 0.34725)115.6798, -72.70831, -32.5494
13generate(0.46221, -0.50134, 0.73145), (-0.05173, 0.8082, 0.58663), (-0.88526, -0.30898, 0.34762)21.09691, 36.90125, -90.66176
14generate(0.40992, 0.5839, 0.70073), (-0.86158, 0.50005, 0.08734), (-0.29941, -0.63954, 0.70806)120.54375, -39.29801, -87.80778
15generate(-0.31545, -0.58376, -0.74814), (-0.58376, -0.50219, 0.63799), (-0.74814, 0.63799, -0.18236)-125.72573, -82.07489, -50.99708
16generate(0.5467, -0.80862, -0.21737), (-0.08248, -0.31034, 0.94704), (-0.83326, -0.49982, -0.23636)-96.82169, -34.80399, -163.39935
17generate(0.99461, 0.08476, 0.05978), (-0.08327, 0.30902, 0.9474), (0.06183, -0.94727, 0.31441)13.59634, 23.64087, -153.60152
18generate(0.5467, -0.08248, -0.83326), (-0.80862, -0.31034, -0.49982), (-0.21737, 0.94704, -0.23636)-86.09325, -170.76348, -26.70562
19generate(0.40929, 0.86177, -0.29972), (-0.58505, 0.49995, 0.63857), (0.70015, -0.08601, 0.7088)52.93629, 12.49093, -35.143
20generate(0.48695, -0.86045, -0.15005), (-0.86045, -0.50209, 0.08683), (-0.15005, 0.08683, -0.98486)-95.42052, -133.85675, -177.99304
21generate(0.98588, 0.05388, 0.15855), (-0.04998, -0.80901, 0.58566), (0.15982, -0.58532, -0.7949)19.94293, -115.70798, -223.44881
22generate(0.46221, -0.05173, -0.88526), (-0.50134, 0.8082, -0.30899), (0.73145, 0.58663, 0.34763)-88.10223, -47.25943, -5.56208
23generate(0.46095, 0.05212, -0.8859), (0.49956, 0.80984, 0.30758), (0.73346, -0.58434, 0.34725)-78.36801, 11.10352, -116.02951
24generate(0.98588, -0.04998, 0.15983), (0.05387, -0.80902, -0.58531), (0.15855, 0.58565, -0.7949)10.26794, -225.47241, -113.01593
25generate(0.483, 0.86291, -0.14869), (0.86291, -0.4979, -0.08652), (-0.14869, -0.08652, -0.98509)67.23309, -149.04076, -194.363
26generate(0.40992, -0.86158, -0.2994), (0.5839, 0.50005, -0.63954), (0.70073, 0.08734, 0.70806)-109.56305, -106.89179, -18.8634
27generate(-0.40139, -0.44845, -0.79861), (0.89317, 0.00141, -0.44971), (0.2028, -0.89381, 0.39998)-117.73056, -135.99566, -140.47953
28generate(-0.40139, 0.89317, 0.2028), (-0.44845, 0.00141, -0.89381), (-0.79861, -0.44971, 0.39998)102.70101, -178.16612, -98.99061
29generate(-0.40037, -0.89436, 0.19955), (0.4486, -0.00141, 0.89373), (-0.79904, 0.44734, 0.40178)-66.18439, -10.45975, -14.22126
30generate(-0.40037, 0.4486, -0.79904), (-0.89436, -0.00141, 0.44734), (0.19955, 0.89373, 0.40178)-33.16928, -52.84589, 28.26938

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Components

#1: Protein VP2 / capsid protein VP2


Mass: 59743.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine parvovirus-1 / Strain: HADEN / Gene: BPV-1 / Plasmid: pFastbac-1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q2LD55, UniProt: G8GWG8*PLUS

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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

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10 mM Tris, 4% PEG8000, 8 mM magnesium chloride, 50 mM lithium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9724 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2007 / Details: mirrors
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 378339 / Num. obs: 340823 / % possible obs: 90.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
3.2-3.312.31.80.365193.2
3.31-3.45177.6
3.45-3.6180.3
3.6-3.79181.5
3.79-4.03182.3
4.03-4.34184.9
4.34-4.78185.8
4.78-5.47185.6
5.47-6.89185.2
6.89-50181.4

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Processing

Software
NameClassification
HKL-2000data collection
PHENIXmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S58

1s58


Resolution: 3.2→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3115 15527 4.1 %RANDOM
Rwork0.3097 295169 --
obs-310696 82.1 %-
Solvent computationBsol: 11.9694 Å2
Displacement parametersBiso max: 123.52 Å2 / Biso mean: 47.6835 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--5.836 Å2-0 Å20 Å2
2--6.462 Å20 Å2
3----0.626 Å2
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3950 0 0 0 3950
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.722
X-RAY DIFFRACTIONc_mcbond_it1.3131.5
X-RAY DIFFRACTIONc_scbond_it1.6162
X-RAY DIFFRACTIONc_mcangle_it2.3812
X-RAY DIFFRACTIONc_scangle_it2.7292.5
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 (%)
3.2-3.310.416614550.4071272482870376.5
3.31-3.450.381314580.3996277592921777.6
3.45-3.60.391315600.3814286743023480.3
3.6-3.790.363515950.3683291263072181.5
3.79-4.030.354614890.3511295333102282.3
4.03-4.340.312615630.3072304793204284.9
4.34-4.780.277616230.2801308073243085.8
4.78-5.470.27515790.2726308323241185.6
5.47-6.890.257516370.2567307843242185.2
6.89-500.232515680.2277299273149581.4
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.paramCNS_TOPPAR:carbohydrate.top

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