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- PDB-5l8q: Structure of deformed wing virus, a honeybee pathogen -

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Basic information

Entry
Database: PDB / ID: 5l8q
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
Apis mellifera (honey bee)
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 8, 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_em_software.details / _em_software.name / _em_software.version

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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-4014
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  • Superimposition on EM map
  • EMDB-4014
  • Imaged by UCSF Chimera
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Movie viewer
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)104,0624
Polyers103,7383
Non-polymers3241
Water0
1
A: VP1
B: VP2
C: VP3
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)6,243,716240
Polyers6,224,265180
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
  • 520 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)520,31020
Polyers518,68915
Non-polymers1,6215
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: VP1
B: VP2
C: VP3
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 624 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)624,37224
Polyers622,42718
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

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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
#4: Chemical ChemComp-U / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Formula: C9H13N2O9P / Source: (natural) Apis mellifera (honey bee) / Uridine monophosphate

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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, 4 / 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 correction
7Cootmodel fitting
9PHENIXmodel refinementReal space refinement
11RELION1.4final Euler assignmentrelion_refine_mpi
12RELION1.4classificationrelion_refine_mpi
13RELION1.43D reconstructionrelion_refine_mpi
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 141860
SymmetryPoint symmetry: I
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 26540 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL / Target criteria: R-factor
RefineOverall SU ML: 1.57 / Sigma F: 0.01 / Overall phase error: 44.53 / 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: 0.342 / R factor R work: 0.3384 / R factor obs: 0.3384 / Highest resolution: 3.2 Å / Lowest resolution: 242.502 Å / Number reflection R free: 2005 / Number reflection obs: 859969 / Percent reflection R free: 0.23 / Percent reflection obs: 99.92
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01036535
ELECTRON MICROSCOPYf_angle_d1.15849825
ELECTRON MICROSCOPYf_dihedral_angle_d10.04413135
ELECTRON MICROSCOPYf_chiral_restr0.0545420
ELECTRON MICROSCOPYf_plane_restr0.0056450
Refine LS shell

Refine ID: ELECTRON MICROSCOPY

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
3.20000.04490.04473.280014461119100.00
3.28000.05100.05223.368714061032100.00
3.36870.05410.05363.467814361081100.00
3.46780.02000.02073.579814361138100.00
3.57980.43120.43533.707714561107100.00
3.70770.45910.37963.856214161091100.00
3.85620.34740.36644.031714261163100.00
4.03170.28940.27194.244314661301100.00
4.24430.22240.23024.510214261175100.00
4.51020.20910.21484.858514661357100.00
4.85850.25880.27265.347414161347100.00
5.34740.23400.25796.121314461515100.00
6.12130.32640.29737.712313861645100.00
7.71230.27970.2333243.20081506189399.00

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