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- EMDB-3574: Structure of deformed wing virus, a honeybee pathogen -

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Basic information

Entry
Database: EMDB / ID: 3574
TitleStructure of deformed wing virus, a honeybee pathogen
Map data
SampleDeformed wing virus:
virus / VP1 / VP2 / VP3 / ligand
Function / homologyHelicase, superfamily 3, single-stranded RNA virus / RNA-directed RNA polymerase, catalytic domain / RNA helicase / 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 / Peptidase S1, PA clan ...Helicase, superfamily 3, single-stranded RNA virus / RNA-directed RNA polymerase, catalytic domain / RNA helicase / 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 / Peptidase S1, PA clan / Picornavirus capsid / RdRp of positive ssRNA viruses catalytic domain profile. / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / CRPV capsid protein like / cysteine-type peptidase activity / RNA helicase activity / viral capsid / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / transcription, DNA-templated / structural molecule activity / RNA binding / ATP binding / Genome polyprotein / Genome polyprotein / Genome polyprotein
Function and homology information
SourceDeformed wing virus
Methodsingle particle reconstruction / cryo EM / 3.1 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: 5mv5

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: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5mv5
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5mv5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3574.map.gz (map file in CCP4 format, 651086 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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.

Voxel sizeX=Y=Z: 1.054 Å
Density
Contour Level:0.07 (by author), 0.07 (movie #1):
Minimum - Maximum-0.38851413 - 0.6225079
Average (Standard dev.)0.0015709469 (0.022487547)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions546546546
Origin-273.0-273.0-273.0
Limit272.0272.0272.0
Spacing546546546
CellA=B=C: 575.484 Å
α=β=γ: 90.0 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-0.3890.6230.002

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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
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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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

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: 21 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 processing

ProcessingMethod: single particle reconstruction / Number of projections: 27130
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: Relion 3D auto refinement
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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