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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
Function / homology
Function and homology information


host cell membrane / viral capsid / host cell cytoplasm / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / proteolysis ...host cell membrane / viral capsid / host cell cytoplasm / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / cytoplasm
Similarity search - Function
Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase ...Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesDeformed wing virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSkubnik, K. / Plevka, P.
Funding support2items
OrganizationGrant numberCountry
European Research Council355855
European Molecular Biology Organization3041
CitationJournal: Curr Opin Virol / Year: 2020
Title: Virion structures and genome delivery of honeybee viruses.
Authors: Michaela Procházková / Karel Škubník / Tibor Füzik / Liya Mukhamedova / Antonín Přidal / Pavel Plevka /
Abstract: The western honeybee is the primary pollinator of numerous food crops. Furthermore, honeybees are essential for ecosystem stability by sustaining the diversity and abundance of wild flowering plants. ...The western honeybee is the primary pollinator of numerous food crops. Furthermore, honeybees are essential for ecosystem stability by sustaining the diversity and abundance of wild flowering plants. However, the worldwide population of honeybees is under pressure from environmental stress and pathogens. Viruses from the families Iflaviridae and Dicistroviridae, together with their vector, the parasitic mite Varroa destructor, are the major threat to the world's honeybees. Dicistroviruses and iflaviruses have capsids with icosahedral symmetries. Acidic pH triggers the genome release of both dicistroviruses and iflaviruses. The capsids of iflaviruses expand, whereas those of dicistroviruses remain compact until the genome release. Furthermore, dicistroviruses use inner capsid proteins, whereas iflaviruses employ protruding domains or minor capsid proteins from the virion surface to penetrate membranes and deliver their genomes into the cell cytoplasm. The structural characterization of the infection process opens up possibilities for the development of antiviral compounds.
History
DepositionDec 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Refinement description / Category: refine

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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
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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
Polymers103,7383
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
Polymers6,224,265180
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
Polymers518,68915
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
Polymers622,42718
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
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Genome polyprotein


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


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


Mass: 46697.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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 / 3D 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: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Deformed wing virus
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Apis mellifera
Virus shellDiameter: 390 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.4
Details: Dulbeccos Phosphate Buffered Saline D8537 sigma aldrich
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Virus was dissolved in PBS buffer.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: 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 X / Calibrated magnification: 74235 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / 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) / Num. 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 selectionNum. of particles selected: 32573
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21000 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
RefinementResolution: 3.1→243.399 Å / SU ML: 0.8 / σ(F): 0.04 / Phase error: 48.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3232 1996 0.21 %
Rwork0.3232 --
obs0.3232 956082 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
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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