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- EMDB-3575: Structure of deformed wing virus, a honeybee pathogen -

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Basic information

Entry
Database: EMDB / ID: 3575
TitleStructure of deformed wing virus, a honeybee pathogen
SampleDeformed wing virus
SourceDeformed wing virus / virus
Map data
Methodsingle particle reconstruction, at 3.5 Å resolution
AuthorsSkubnik K / Novacek J
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, 3210-3215

Proc. Natl. Acad. Sci. U.S.A., 2017, 114, 3210-3215 Yorodumi Papers
Structure of deformed wing virus, a major honey bee pathogen.
Karel Škubník / Jiří Nováček / Tibor Füzik / Antonín Přidal / Robert J Paxton / Pavel Plevka

Validation ReportPDB-ID: 5mv6

SummaryFull reportAbout validation report
DateDeposition: Jan 15, 2017 / Header (metadata) release: Aug 31, 2016 / Map release: Apr 5, 2017 / Last update: Aug 30, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 0.055
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5mv6
  • Surface level: 0.055
  • Imaged by UCSF CHIMERA
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5mv6
  • Imaged by Jmol
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Supplemental images

Downloads & links

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Map

Fileemd_3575.map.gz (map file in CCP4 format, 651086 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
546 pix
1.05 Å/pix.
= 575.484 Å
546 pix
1.05 Å/pix.
= 575.484 Å
546 pix
1.05 Å/pix.
= 575.484 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.054 Å
Density
Contour Level:0.055 (by author), 0.055 (movie #1):
Minimum - Maximum-0.14610638 - 0.22774634
Average (Standard dev.)0.0023943996 (0.012725688)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions546546546
Origin-273-273-273
Limit272272272
Spacing546546546
CellA=B=C: 575.484 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0541.0541.054
M x/y/z546546546
origin x/y/z0.0000.0000.000
length x/y/z575.484575.484575.484
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-273-273-273
NC/NR/NS546546546
D min/max/mean-0.1460.2280.002

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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: 5

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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 / virus
Source (natural)Host Species: Apis mellifera / arthropod / セイヨウミツバチ, ヨウシュミツバチ /

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Component #2: protein, VP1

ProteinName: VP1 / Recombinant expression: No
MassTheoretical: 28.679273 kDa
SourceSpecies: Deformed wing virus / virus

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Component #3: protein, VP2

ProteinName: VP2 / Recombinant expression: No
MassTheoretical: 28.3609 kDa
SourceSpecies: Deformed wing virus / virus

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Component #4: protein, VP3

ProteinName: VP3 / Recombinant expression: No
MassTheoretical: 46.697582 kDa
SourceSpecies: Deformed wing virus / virus

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Component #5: ligand, URIDINE-5'-MONOPHOSPHATE

LigandName: URIDINE-5'-MONOPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.324181 kDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 2.5 mg/ml
Buffer solution: Dulbeccos Phosphate Buffered Saline D8537 sigma aldrich
pH: 5
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: 21 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 75000 X (nominal), 74235 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 4000 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: 3000

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 945
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: Relion 3D auto refinement
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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