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- PDB-5mv5: Structure of deformed wing virus, a honeybee pathogen -

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Basic information

Entry
Database: PDB / ID: 5mv5
TitleStructure of deformed wing virus, a honeybee pathogen
DescriptorVP1, vp2, vp3
KeywordsVIRAL PROTEIN / Deformed wing virus / Picornavirales / Iflaviridae / Iflavirus / viral protein
Specimen sourceDeformed wing virus / virus
MethodElectron microscopy (3.1 A resolution / Single particle)
AuthorsSkubnik, K. / Novacek, J. / Fuzik, T. / Pridal, A. / Paxton, R. / Plevka, P.
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, 3210-3215

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

DateDeposition: Jan 15, 2017 / Release: Apr 5, 2017

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-3574
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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,0624
Polyers103,7383
Non-polymers3241
Water0
#1
A: VP1
B: VP2
C: VP3
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)6,243,716240
Polyers6,224,265180
Non-polymers19,45160
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
#2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
#3
A: VP1
B: VP2
C: VP3
hetero molecules
x 5


  • icosahedral pentamer
  • 520 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)520,31020
Polyers518,68915
Non-polymers1,6215
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#4
A: VP1
B: VP2
C: VP3
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 624 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)624,37224
Polyers622,42718
Non-polymers1,9456
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

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Components

#1: Polypeptide(L)VP1


Mass: 28679.273 Da / Num. of mol.: 1 / Source: (natural) Deformed wing virus / virus / References: UniProt: L0CTV4
#2: Polypeptide(L)VP2


Mass: 28360.900 Da / Num. of mol.: 1 / Source: (natural) Deformed wing virus / virus / References: UniProt: E0YTW0
#3: Polypeptide(L)VP3


Mass: 46697.582 Da / Num. of mol.: 1 / Source: (natural) Deformed wing virus / virus / References: UniProt: Q7TG18
#4: ChemicalChemComp-U / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Formula: C9H13N2O9P

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Deformed wing virus / Details: Virus was purified from honeybee pupae. / Type: VIRUS
Details of the virusEmpty: NO / Enveloped: NO / Virus isolate: OTHER / Virus type: VIRION
Buffer solutionDetails: Dulbeccos Phosphate Buffered Saline D8537 sigma aldrich
Specimen supportGrid material: COPPER / Grid mesh size: 300 /inch. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Calibrated magnification: 74235 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER

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Processing

3D reconstructionResolution: 3.1 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 27130 / Number of class averages: 1
Atomic model buildingRef protocol: OTHER / Ref space: REAL / Target criteria: R factor

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