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- EMDB-4009: Structure of deformed wing virus, a honeybee pathogen -

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Basic information

Entry
Database: EMDB / ID: 4009
TitleStructure of deformed wing virus, a honeybee pathogen
Map dataMap of full particle of deformed wing virus.
SampleDeformed wing virus:
virus / VP1 / vp2 / vp3
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 / structural molecule activity / transcription, DNA-templated / RNA binding / membrane / ATP binding / Genome polyprotein / Genome polyprotein / Genome polyprotein / Genome polyprotein
Function and homology information
SourceDeformed wing virus
Methodsingle 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 ReportPDB-ID: 5l7q

SummaryFull reportAbout validation report
DateDeposition: Jun 3, 2016 / Header (metadata) release: Aug 31, 2016 / Map release: Mar 29, 2017 / Last update: Aug 30, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 51
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 51
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5l7q
  • Surface level: 51
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5l7q
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4009.map.gz (map file in CCP4 format, 536871 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.06 Å/pix.
= 542.208 Å
512 pix
1.06 Å/pix.
= 542.208 Å
512 pix
1.06 Å/pix.
= 542.208 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density
Contour Level:51.0 (by author), 51 (movie #1):
Minimum - Maximum-399.400449999999978 - 534.262449999999944
Average (Standard dev.)-0.02670613 (22.60866)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions512512512
Origin-256.0-256.0-256.0
Limit255.0255.0255.0
Spacing512512512
CellA=B=C: 542.208 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z542.208542.208542.208
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-256-256-256
NC/NR/NS512512512
D min/max/mean-399.400534.262-0.027

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Supplemental data

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Sample components

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Entire Deformed wing virus

EntireName: Deformed wing virus / Details: Virus was purified from honeybee pupae / Number of components: 4

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Component #1: virus, Deformed wing virus

VirusName: Deformed wing virus / Class: VIRION / Details: Virus was purified from honeybee pupae / Empty: No / Enveloped: No / Isolate: OTHER
SpeciesSpecies: Deformed wing virus
Source (natural)Host Species: Apis mellifera (honey bee)

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Component #2: protein, VP1

ProteinName: VP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.679273 kDa
SourceSpecies: Deformed wing virus

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Component #3: protein, vp2

ProteinName: vp2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.3609 kDa
SourceSpecies: Deformed wing virus

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Component #4: protein, vp3

ProteinName: vp3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.697582 kDa
SourceSpecies: Deformed wing virus

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 2.5 mg/ml
Buffer solution: Dulbeccos Phosphate Buffered Saline D8537 sigma aldrich
pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 75000.0 X (nominal), 74235.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 4000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 26

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 136828
3D reconstructionSoftware: j3dr / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Target criteria: R-factor / Refinement space: REAL
Output model

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