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- EMDB-3570: Structure of deformed wing virus, a honeybee pathogen -

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Basic information

Entry
Database: EMDB / ID: 3570
TitleStructure of deformed wing virus, a honeybee pathogen
Map data
SampleDeformed wing virus
  • virus
  • VP1
  • VP2
  • VP3
  • ligand
Function/homologyDicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / cysteine-type peptidase activity / Picornavirus capsid / 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 / host cell membrane / Picornavirus/Calicivirus coat protein ...Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / cysteine-type peptidase activity / Picornavirus capsid / 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 / host cell membrane / Picornavirus/Calicivirus coat protein / RNA-directed RNA polymerase, C-terminal domain / RNA dependent RNA polymerase / RNA helicase activity / viral capsid / picornavirus capsid protein / RdRp of positive ssRNA viruses catalytic domain profile. / RNA-directed RNA polymerase, catalytic domain / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / Peptidase S1, PA clan / structural molecule activity / P-loop containing nucleoside triphosphate hydrolase / transcription, DNA-templated / RNA binding / membrane / ATP binding / Genome polyprotein / Genome polyprotein / Genome polyprotein
Function and homology information
SourceDeformed wing virus / / virus
MethodCryo EM / single particle reconstruction / 3.8 Å resolution
AuthorsSkubnik K / Novacek J
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
Abstract: The worldwide population of western honey bees () is under pressure from habitat loss, environmental stress, and pathogens, particularly viruses that cause lethal epidemics. Deformed wing virus (DWV) ...The worldwide population of western honey bees () is under pressure from habitat loss, environmental stress, and pathogens, particularly viruses that cause lethal epidemics. Deformed wing virus (DWV) from the family , together with its vector, the mite , is likely the major threat to the world's honey bees. However, lack of knowledge of the atomic structures of iflaviruses has hindered the development of effective treatments against them. Here, we present the virion structures of DWV determined to a resolution of 3.1 Å using cryo-electron microscopy and 3.8 Å by X-ray crystallography. The C-terminal extension of capsid protein VP3 folds into a globular protruding (P) domain, exposed on the virion surface. The P domain contains an Asp-His-Ser catalytic triad that is, together with five residues that are spatially close, conserved among iflaviruses. These residues may participate in receptor binding or provide the protease, lipase, or esterase activity required for entry of the virus into a host cell. Furthermore, nucleotides of the DWV RNA genome interact with VP3 subunits. The capsid protein residues involved in the RNA binding are conserved among honey bee iflaviruses, suggesting a putative role of the genome in stabilizing the virion or facilitating capsid assembly. Identifying the RNA-binding and putative catalytic sites within the DWV virion structure enables future analyses of how DWV and other iflaviruses infect insect cells and also opens up possibilities for the development of antiviral treatments.
Validation ReportPDB-ID: 5mup

SummaryFull reportAbout validation report
DateDeposition: Jan 13, 2017 / Header (metadata) release: Aug 31, 2016 / Map release: Apr 5, 2017 / Last update: Aug 2, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.045
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5mup
  • Surface level: 0.045
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5mup
  • Imaged by Jmol
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3D viewer
Supplemental images

Downloads & links

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Map

Fileemd_3570.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 package.

Voxel sizeX=Y=Z: 1.054 Å
Density
Contour Level:0.045 (by author), 0.045 (movie #1):
Minimum - Maximum-0.2114736 - 0.32601574
Average (Standard dev.)0.0012782764 (0.014463036)
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-0.2110.3260.001

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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 / Western honey bee / arthropod /

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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

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 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 processing

ProcessingMethod: single particle reconstruction / Number of projections: 879
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.8 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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