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

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Basic information

Entry
Database: EMDB / ID: EMD-3574
TitleStructure of deformed wing virus, a honeybee pathogen
Map data
Sample
  • Virus: Deformed wing virus
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
  • Ligand: URIDINE-5'-MONOPHOSPHATE
KeywordsDeformed wing virus / Picornavirales / Iflaviridae / Iflavirus / viral protein
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
Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesDeformed wing virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSkubnik K / Novacek J
Funding support2 items
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
Header (metadata) releaseAug 31, 2016-
DepositionJan 15, 2017-
Map releaseApr 5, 2017-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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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 modelsPDB-5mv5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3574.png

Downloads & links

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Map

FileDownload / File: emd_3574.map.gz / Format: CCP4 / Size: 620.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 546 pix.
= 575.484 Å		1.05 Å/pix.
x 546 pix.
= 575.484 Å		1.05 Å/pix.
x 546 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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.38851413 - 0.6225079
Average (Standard dev.)0.0015709469 (±0.022487547)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-273-273-273
Dimensions546546546
Spacing546546546
CellA=B=C: 575.484 Å
α=β=γ: 90.0 °

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
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
Components
  • Virus: Deformed wing virus
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
  • Ligand: URIDINE-5'-MONOPHOSPHATE

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Supramolecule #1: Deformed wing virus

SupramoleculeName: Deformed wing virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: Virus was purified from honeybee pupae. / NCBI-ID: 198112 / Sci species name: Deformed wing virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Apis mellifera (honey bee)
Virus shellShell ID: 1 / Diameter: 390.0 Å / T number (triangulation number): 3

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Deformed wing virus
Molecular weightTheoretical: 28.679273 KDa
SequenceString: GEESRNTTVL DTTTTLQSSG FGRAFFGEAF NDLKTLMRRY QLYGQLLLSV TTDKDIDHCM FTFPCLPQGL ALDIGSAGSP HEIFNRCRD GIIPLIASGY RFYRGDLRYK IVFPSNVNSN IWVQHRPDRR LEGWSAAKIV NCDAVSTGQG VYNHGYASHI Q ITRVNNVI ...String:
GEESRNTTVL DTTTTLQSSG FGRAFFGEAF NDLKTLMRRY QLYGQLLLSV TTDKDIDHCM FTFPCLPQGL ALDIGSAGSP HEIFNRCRD GIIPLIASGY RFYRGDLRYK IVFPSNVNSN IWVQHRPDRR LEGWSAAKIV NCDAVSTGQG VYNHGYASHI Q ITRVNNVI ELEVPFYNAT CYNYLQAFNA SSAASSYAVS LGEISVGFQA TSDDIASIVN KPVTIYYSIG DGMQFSQWVG YQ PMMILDQ LPAPVVRAVP E

UniProtKB: Genome polyprotein

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Macromolecule #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Deformed wing virus
Molecular weightTheoretical: 28.3609 KDa
SequenceString: MDNPNPGPDG EGEVELEKDS NVVLTTQRDP STSIPAPVSV KWSRWTSNDV VDDYATITSR WYQIAEFVWS KDDPFDKELA RLILPRALL SSIEANSDAI CDVPNTIPFK VHAYWRGDME VRVQINSNKF QVGQLQATWY YSDHENLNIS SKRSVYGFSQ M DHALISAS ...String:
MDNPNPGPDG EGEVELEKDS NVVLTTQRDP STSIPAPVSV KWSRWTSNDV VDDYATITSR WYQIAEFVWS KDDPFDKELA RLILPRALL SSIEANSDAI CDVPNTIPFK VHAYWRGDME VRVQINSNKF QVGQLQATWY YSDHENLNIS SKRSVYGFSQ M DHALISAS ASNEAKLVIP FKHVYPFLPT RIVPDWTTGI LDMGALNIRV IAPLRMSATG PTTCNVVVFI KLNNSEFTGT SS GKFYASQ IRAKPE

UniProtKB: Genome polyprotein

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Macromolecule #3: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Deformed wing virus
Molecular weightTheoretical: 46.697582 KDa
SequenceString: DNPSYQQSPR HFVPTGMHSL ALGTNLVEPL HALRLDAAGT TQHPVGCAPD EDMTVSSIAS RYGLIRRVQW KKDHAKGSLL LQLDADPFV EQRIEGTNPI SLYWFAPVGV VSSMFMQWRG SLEYRFDIIA SQFHTGRLIV GYVPGLTASL QLQMDYMKLK S SSYVVFDL ...String:
DNPSYQQSPR HFVPTGMHSL ALGTNLVEPL HALRLDAAGT TQHPVGCAPD EDMTVSSIAS RYGLIRRVQW KKDHAKGSLL LQLDADPFV EQRIEGTNPI SLYWFAPVGV VSSMFMQWRG SLEYRFDIIA SQFHTGRLIV GYVPGLTASL QLQMDYMKLK S SSYVVFDL QESNSFTFEV PYVSYRPWWV RKYGGNYLPS STDAPSTLFM YVQVPLIPME AVSDTIDINV YVRGGSSFEV CV PVQPSLG LNWNTDFILR NDEEYRAKTG YAPYYAGVWH SFNNSNSLVF RWGSASDQIA QWPTISVPRG ELAFLRIKDG KQA AVGTQP WRTMVVWPSG HGYNIGIPTY NAERARQLAQ HLYGGGSLTD EKAKQLFVPA NQQGPGKVSN GNPVWEVMRA PLAT QRAHI QDFEFIEAIP E

UniProtKB: Genome polyprotein

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Macromolecule #4: URIDINE-5'-MONOPHOSPHATE

MacromoleculeName: URIDINE-5'-MONOPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: U
Molecular weightTheoretical: 324.181 Da
Chemical component information

ChemComp-U:
URIDINE-5'-MONOPHOSPHATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.5 mg/mL
BufferpH: 7.4
Details: Dulbeccos Phosphate Buffered Saline D8537 sigma aldrich
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: NITROGEN / Pretreatment - Pressure: 0.007 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
DetailsVirus 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.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 2-16 / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 21.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 74235 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 75169
Startup modelType of model: OTHER
Details: Model obtained from previous single particle reconstruction of DWV and low-pass filtered to resolution 40.
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Software - details: relion_refine_mpi / Number images used: 27130
Initial angle assignmentType: OTHER
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4) / Software - details: relion_refine_mpi / Details: Relion 3D auto refinement
Final 3D classificationNumber classes: 5 / Avg.num./class: 18000 / Software - Name: RELION (ver. 1.4) / Software - details: relion_refine_mpi
Details: Relion 3D classfication - reclassification after initial 3D refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Target criteria: R-factor
Output model

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

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