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- PDB-5g52: Crystallographic structure of full particle of Deformed Wing Virus -

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Basic information

Entry
Database: PDB / ID: 5g52
TitleCrystallographic structure of full particle of Deformed Wing Virus
Components
  • VP1
  • VP2
  • VP3
KeywordsVIRUS / PICORNAVIRALES / IFLAVIRIDAE / IFLAVIRUS / DWV CAPSID / P JELLYROLL / CATALYTIC SITE PROTEASE / LIPASE ESTERASE RECEPTO
Function / homologyRNA-directed RNA polymerase, catalytic domain / CRPV capsid protein like / RNA dependent RNA polymerase / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / P-loop containing nucleoside triphosphate hydrolase / Dicistrovirus, capsid-polyprotein, C-terminal / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan ...RNA-directed RNA polymerase, catalytic domain / CRPV capsid protein like / RNA dependent RNA polymerase / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / P-loop containing nucleoside triphosphate hydrolase / Dicistrovirus, capsid-polyprotein, C-terminal / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / RdRp of positive ssRNA viruses catalytic domain profile. / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RNA helicase / cysteine-type peptidase activity / host cell membrane / RNA helicase activity / viral capsid / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / transcription, DNA-templated / structural molecule activity / RNA binding / membrane / ATP binding / Genome polyprotein
Function and homology information
Specimen sourceDEFORMED WING VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 3.802 Å resolution
AuthorsSkubnik, K. / Novacek, J. / Fuzik, T. / Pridal, A. / Paxton, R. / Plevka, P.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structure of deformed wing virus, a major honey bee pathogen.
Authors: Karel Škubník / Jiří Nováček / Tibor Füzik / Antonín Přidal / Robert J Paxton / Pavel Plevka
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 18, 2016 / Release: Mar 22, 2017
RevisionDateData content typeGroupProviderType
1.0Mar 22, 2017Structure modelrepositoryInitial release
1.1Mar 29, 2017Structure modelDatabase references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9364
Polyers99,6123
Non-polymers3241
Water0
1
A: VP1
B: VP2
C: VP3
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,996,189240
Polyers5,976,738180
Non-polymers19,45160
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: VP1
B: VP2
C: VP3
hetero molecules
x 5


  • icosahedral pentamer
  • 500 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)499,68220
Polyers498,06115
Non-polymers1,6215
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: VP1
B: VP2
C: VP3
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 600 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)599,61924
Polyers597,67418
Non-polymers1,9456
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
Unit cell
γ
α
β
Length a, b, c (Å)360.131, 360.131, 360.131
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI 2 3

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Components

#1: Protein/peptide VP1


Mass: 27123.602 Da / Num. of mol.: 1 / Source: (natural) DEFORMED WING VIRUS / References: UniProt: Q8B3M2*PLUS
#2: Protein/peptide VP2


Mass: 28005.490 Da / Num. of mol.: 1 / Source: (natural) DEFORMED WING VIRUS / References: UniProt: Q8B3M2*PLUS
#3: Protein/peptide VP3


Mass: 44483.203 Da / Num. of mol.: 1 / Source: (natural) DEFORMED WING VIRUS / References: UniProt: Q8B3M2*PLUS
#4: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Formula: C9H13N2O9P / Uridine monophosphate
Sequence detailsSEQUENCE TO THE UNIPROT WILL BE UPLOAD SOON.

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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

CrystalDescription: MODEL WAS USED FROM CRYOEM RECONSTRUCTION
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 0.8 M POTASSIUM DIHYDROGEN PHOSPHATE, 0.8 M SODIUM DIHYDROGEN PHOSPHATE, 0.1 M SODIUM HEPES, 7.5 PH

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Data collection

DiffractionMean temperature: 100
SourceSource: SYNCHROTRON / Type: SOLEIL BEAMLINE PROXIMA 1 / Synchrotron site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857
DetectorType: DECTRIS PILATUS 6M
Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL
Detector: PIXEL
RadiationMonochromator: CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 / Relative weight: 1
ReflectionD resolution high: 3.8 / D resolution low: 29.8 / Number obs: 56889 / Observed criterion sigma I: 0.9 / Rmerge I obs: 0.37 / NetI over sigmaI: 2 / Redundancy: 1.8 % / Percent possible obs: 75.7
Reflection shellRmerge I obs: 0.8 / Highest resolution: 3.8 / Lowest resolution: 3.91 / MeanI over sigI obs: 0.9 / Redundancy: 1.78 % / Percent possible all: 76.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT / Overall SU ML: 0.68 / Sigma F: 1.36 / Overall phase error: 34.06 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 / Solvent vdw probe radii: 1.11 / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.3224 / R factor R work: 0.2828 / R factor obs: 0.2849 / Highest resolution: 3.802 / Lowest resolution: 29.805 / Number reflection R free: 2844 / Number reflection obs: 56873 / Percent reflection R free: 5 / Percent reflection obs: 75.04
Refine hist #LASTHighest resolution: 3.802 / Lowest resolution: 29.805
Number of atoms included #LASTProtein: 7025 / Nucleic acid: 0 / Ligand: 20 / Solvent: 0 / Total: 7045
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00836215
X-RAY DIFFRACTIONf_angle_d1.46649380
X-RAY DIFFRACTIONf_dihedral_angle_d16.21513010
X-RAY DIFFRACTIONf_chiral_restr0.0555355
X-RAY DIFFRACTIONf_plane_restr0.0066385
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
3.80160.40540.35653.8670143267375.00
3.86700.34900.34453.9372131273277.00
3.93720.37040.32914.0127154269776.00
4.01270.34850.31704.0944130270075.00
4.09440.35750.31484.1832144274376.00
4.18320.32830.30684.2803146272076.00
4.28030.29430.28934.3870151273376.00
4.38700.31590.27384.5052133276978.00
4.50520.30690.27834.6373151270276.00
4.63730.33020.27184.7864150277777.00
4.78640.32850.26854.9567133276477.00
4.95670.31670.27095.1542140272776.00
5.15420.30000.27105.3875135275076.00
5.38750.35190.26785.6697144270175.00
5.66970.34730.28886.0222143271276.00
6.02220.29240.27156.4828149275777.00
6.48280.29330.26537.1271159273175.00
7.12710.28360.24648.1400129264173.00
8.14000.24810.219210.1870131258371.00
10.18700.32550.257829.8056148241766.00

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