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- PDB-5l7q: Structure of deformed wing virus, a honeybee pathogen -

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Basic information

Entry
Database: PDB / ID: 5l7q
TitleStructure of deformed wing virus, a honeybee pathogen
Components
  • VP1
  • vp2
  • vp3
KeywordsVIRAL PROTEIN / Deformed wing virus / Picornavirales / Iflaviridae / Iflavirus / viral protein
Function / homologyPeptidase S1, PA clan / 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 / RNA-directed RNA polymerase, catalytic domain ...Peptidase S1, PA clan / 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 / RNA-directed RNA polymerase, catalytic domain / 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 / Genome polyprotein / Genome polyprotein / Genome polyprotein
Function and homology information
Specimen sourceDeformed wing virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.5 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: Jun 3, 2016 / Release: Mar 29, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 29, 2017Structure modelrepositoryInitial release
1.1Aug 2, 2017Structure modelData collection / Refinement descriptionem_3d_fitting / em_software_em_3d_fitting.target_criteria / _em_software.name / _em_software.version
1.2Aug 30, 2017Structure modelData collectionem_software

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • EMDB-4009
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-4009
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP1
B: vp2
C: vp3


Theoretical massNumber of molelcules
Total (without water)103,7383
Polyers103,7383
Non-polymers00
Water0
1
A: VP1
B: vp2
C: vp3
x 60


Theoretical massNumber of molelcules
Total (without water)6,224,265180
Polyers6,224,265180
Non-polymers00
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
x 5


  • icosahedral pentamer
  • 519 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)518,68915
Polyers518,68915
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: VP1
B: vp2
C: vp3
x 6


  • icosahedral 23 hexamer
  • 622 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)622,42718
Polyers622,42718
Non-polymers00
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

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Components

#1: Protein/peptide VP1


Mass: 28679.273 Da / Num. of mol.: 1 / Source: (natural) Deformed wing virus / References: UniProt: L0CTV4
#2: Protein/peptide vp2


Mass: 28360.900 Da / Num. of mol.: 1 / Source: (natural) Deformed wing virus / References: UniProt: E0YTW0, UniProt: Q8B3M2*PLUS
#3: Protein/peptide vp3


Mass: 46697.582 Da / Num. of mol.: 1 / Source: (natural) Deformed wing virus / References: UniProt: Q7TG18, UniProt: Q8B3M2*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Deformed wing virus / Type: VIRUS / Details: Virus was purified from honeybee pupae / Entity ID: 1, 2, 3 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Deformed wing virus
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: OTHER / Virus type: VIRION
Natural hostOrganism: Apis mellifera
Virus shellDiameter: 390 nm / Triangulation number (T number): 3
Buffer solutionDetails: Dulbeccos Phosphate Buffered Saline D8537 sigma aldrich
pH: 7.4
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 / Calibrated magnification: 74235 / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 15 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Number of grids imaged: 1 / Number of real images: 26
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 7 / Used frames/image: 2-7

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EMAN2particle selectione2boxer.py
2EPUimage acquisition
4CTFFIND4CTF correctionCTFFIND4, Grigorieff lab
7Cootmodel fitting
9jaligninitial Euler assignmentjalign, Jiang lab
10jalingnfinal Euler assignmentjalign, Jiang lab
11commonImagesclassificationcommonImages.py, Jiang lab
12j3dr3D reconstructionj3dr
13PHENIXmodel refinementReal space refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 141860
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 136828 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL / Target criteria: R-factor
RefineOverall SU ML: 0.7 / Sigma F: 0.01 / Overall phase error: 40.76 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.3395 / R factor R work: 0.2983 / R factor obs: 0.2984 / Highest resolution: 3.44 Å / Lowest resolution: 542.25 Å / Number reflection R free: 2001 / Number reflection obs: 692955 / Percent reflection R free: 0.29 / Percent reflection obs: 99.93
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01236454
ELECTRON MICROSCOPYf_angle_d1.15149696
ELECTRON MICROSCOPYf_dihedral_angle_d9.80913081
ELECTRON MICROSCOPYf_chiral_restr0.0585395
ELECTRON MICROSCOPYf_plane_restr0.0066445
Refine LS shell

Refine ID: ELECTRON MICROSCOPY

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
3.44010.53830.63493.526114249244100.00
3.52610.44870.44673.621514049126100.00
3.62150.41520.39873.728114349153100.00
3.72810.43090.38533.848413749252100.00
3.84840.39170.41763.986014549202100.00
3.98600.33810.34304.145614149165100.00
4.14560.35970.30824.334314349310100.00
4.33430.33560.27904.562814549323100.00
4.56280.32220.26734.848714649289100.00
4.84870.30140.28195.223114149342100.00
5.22310.34540.29215.748714249463100.00
5.74870.34000.31566.580714249467100.00
6.58070.26480.28568.291114349680100.00
8.29110.35940.2866549.11431514993899.00

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