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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
Components
  • VP1
  • VP2
  • VP3
KeywordsVIRAL PROTEIN / Deformed wing virus / Picornavirales / Iflaviridae / Iflavirus
Function / homology
Function and homology information


host cell membrane / viral capsid / host cell cytoplasm / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / proteolysis ...host cell membrane / viral capsid / host cell cytoplasm / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / cytoplasm
Similarity search - Function
Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / 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 ...Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / 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 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
URIDINE-5'-MONOPHOSPHATE / Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesDeformed wing virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSkubnik, K. / Novacek, J. / Fuzik, T. / Pridal, A. / Paxton, R. / Plevka, P.
Funding support2items
OrganizationGrant numberCountry
European Research Council355855
European Molecular Biology Organization3041
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.
History
DepositionJan 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_software
Item: _em_3d_fitting.target_criteria / _em_software.name / _em_software.version
Revision 1.2Aug 30, 2017Group: Data collection / Category: em_software
Item: _em_software.details / _em_software.name / _em_software.version
Revision 1.3May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • 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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  • Superimposition on EM map
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Movie viewer
Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)104,0624
Polymers103,7383
Non-polymers3241
Water00
1
A: VP1
B: VP2
C: VP3
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)6,243,716240
Polymers6,224,265180
Non-polymers19,45160
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
Polymers518,68915
Non-polymers1,6215
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
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
Polymers622,42718
Non-polymers1,9456
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein VP1


Mass: 28679.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deformed wing virus / References: UniProt: L0CTV4
#2: Protein VP2


Mass: 28360.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deformed wing virus / References: UniProt: E0YTW0, UniProt: Q7TG18*PLUS
#3: Protein VP3


Mass: 46697.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deformed wing virus / References: UniProt: Q7TG18
#4: Chemical ChemComp-U / URIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Deformed wing virus / Type: VIRUS / Details: Virus was purified from honeybee pupae. / Entity ID: #1-#3 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Deformed wing virus
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Apis mellifera
Virus shellDiameter: 390 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.4
Details: Dulbeccos Phosphate Buffered Saline D8537 sigma aldrich
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Virus was incubated in high salt solution containing 0.8 M potassium dihydrogen phosphate, 0.8 M sodium dihydrogen phosphate, 0.1 M sodium HEPES, pH 7.5. After 12 hours incubation ...Details: Virus was incubated in high salt solution containing 0.8 M potassium dihydrogen phosphate, 0.8 M sodium dihydrogen phosphate, 0.1 M sodium HEPES, pH 7.5. After 12 hours incubation glutaraldehyde was added to final concentration 1%. After 1 hour was virus dialysed into PBS buffer.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: 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 / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 21 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 16 / Used frames/image: 2-16

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN2particle selectione2boxer.py
2EPUimage acquisition
4CTFFIND4CTF correction
7Cootmodel fitting
9PHENIXmodel refinementReal space refinement
11RELION1.4final Euler assignmentrelion_refine_mpi
12RELION1.4classificationrelion_refine_mpi
13RELION1.43D reconstructionrelion_refine_mpi
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 75169
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27130 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: R-factor

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