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- PDB-6f5j: Structure of deformed wing virus carrying the GFP gene -

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Basic information

Entry
Database: PDB / ID: 6f5j
TitleStructure of deformed wing virus carrying the GFP gene
Components(Genome polyprotein) x 3
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
Function and homology information
Specimen sourceDeformed wing virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.1 Å resolution
AuthorsSkubnik, K. / Plevka, P.
CitationJournal: To Be Published
Title: In vivo infection dynamics of deformed wing virus (DWV) in honeybees
Authors: Skubnik, K. / Plevka, P.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 1, 2017 / Release: Dec 12, 2018

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-4189
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  • Superimposition on EM map
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  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)103,7383
Polyers103,7383
Non-polymers00
Water0
1
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
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: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
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: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
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 Genome polyprotein


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


Mass: 28360.900 Da / Num. of mol.: 1 / Source: (natural) Deformed wing virus / References: UniProt: E0YTW0
#3: Protein/peptide Genome polyprotein


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

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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 / Details: Virus was dissolved in PBS buffer. / 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: 100 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 21 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Number of grids imaged: 1
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 16 / Used frames/image: 2-16

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Processing

SoftwareName: PHENIX / Version: (1.12rc0_2787: ???) / Classification: refinement
EM software
IDNameVersionCategoryDetails
2EPUimage acquisition
4GctfCTF correction
7Cootmodel fitting
10RELION2.1final Euler assignmentrelion_refine_mpi
11RELION1.4classificationrelion_refine_mpi
12RELION2.13D reconstructionrelion_refine_mpi
13PHENIXmodel refinementReal space refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 32573
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 21000 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL
Refine
Refine IDR factor R freeR factor R workR factor obsHighest resolutionLowest resolutionNumber reflection R freeNumber reflection obsPercent reflection R freePercent reflection obsOverall SU MLSigma FOverall phase errorSolvent shrinkage radiiSolvent vdw probe radiiStereochemistry target valuesSolvent model details
10.32320.32320.32323.100243.39919969560820.2199.920.800.0448.020.901.11MLFLAT BULK SOLVENT MODEL
ELECTRON MICROSCOPY
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00636190
ELECTRON MICROSCOPYf_angle_d1.06549365
ELECTRON MICROSCOPYf_dihedral_angle_d11.39112910
ELECTRON MICROSCOPYf_chiral_restr0.0975390
ELECTRON MICROSCOPYf_plane_restr0.0076375

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