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- EMDB-0298: Virus-like Particles based on Potato Virus Y -

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Basic information

Entry
Database: EMDB / ID: EMD-0298
TitleVirus-like Particles based on Potato Virus Y
Map dataCryoEM map of Virus-Like Particle from Potato virus Y
Sample
  • Complex: Virus-like Particle based on Potato Virus Y
    • Complex: Coat protein of Potato Virus Y
      • Protein or peptide: Polyprotein
KeywordsVirus-like Particle / Potyvirus / flexuous filaments / stacked-ring assembly / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / host cell cytoplasmic vesicle / helical viral capsid / serine-type peptidase activity / helicase activity / vesicle / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription ...hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / host cell cytoplasmic vesicle / helical viral capsid / serine-type peptidase activity / helicase activity / vesicle / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Helper component proteinase / Peptidase S30, polyprotein P1, potyvirus / Polyprotein, Potyviridae / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain / Potyviral polyprotein protein 3 / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain superfamily / Helper component proteinase / Peptidase family C4 / Potyvirus P1 protease / Potyviridae polyprotein ...Helper component proteinase / Peptidase S30, polyprotein P1, potyvirus / Polyprotein, Potyviridae / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain / Potyviral polyprotein protein 3 / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain superfamily / Helper component proteinase / Peptidase family C4 / Potyvirus P1 protease / Potyviridae polyprotein / Protein P3 of Potyviral polyprotein / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain profile. / Potyviridae P1 protease domain profile. / Potyvirus NIa protease (NIa-pro) domain / Potyvirus NIa protease (NIa-pro) domain profile. / Potyvirus coat protein / Potyvirus coat protein / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / 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
Biological speciesPotato virus Y
Methodhelical reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsPodobnik M / Kezar A
Funding support Slovenia, Czech Republic, 3 items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0391 Slovenia
Slovenian Research AgencyJ7-7248 Slovenia
Ministry of Education, Youth and Sports of the Czech RepublicLM2015043 Czech Republic
CitationJournal: Sci Adv / Year: 2019
Title: Structural basis for the multitasking nature of the potato virus Y coat protein.
Authors: Andreja Kežar / Luka Kavčič / Martin Polák / Jiří Nováček / Ion Gutiérrez-Aguirre / Magda Tušek Žnidarič / Anna Coll / Katja Stare / Kristina Gruden / Maja Ravnikar / David ...Authors: Andreja Kežar / Luka Kavčič / Martin Polák / Jiří Nováček / Ion Gutiérrez-Aguirre / Magda Tušek Žnidarič / Anna Coll / Katja Stare / Kristina Gruden / Maja Ravnikar / David Pahovnik / Ema Žagar / Franci Merzel / Gregor Anderluh / Marjetka Podobnik /
Abstract: Potato virus Y (PVY) is among the most economically important plant pathogens. Using cryoelectron microscopy, we determined the near-atomic structure of PVY's flexuous virions, revealing a previously ...Potato virus Y (PVY) is among the most economically important plant pathogens. Using cryoelectron microscopy, we determined the near-atomic structure of PVY's flexuous virions, revealing a previously unknown lumenal interplay between extended carboxyl-terminal regions of the coat protein units and viral RNA. RNA-coat protein interactions are crucial for the helical configuration and stability of the virion, as revealed by the unique near-atomic structure of RNA-free virus-like particles. The structures offer the first evidence for plasticity of the coat protein's amino- and carboxyl-terminal regions. Together with mutational analysis and in planta experiments, we show their crucial role in PVY infectivity and explain the ability of the coat protein to perform multiple biological tasks. Moreover, the high modularity of PVY virus-like particles suggests their potential as a new molecular scaffold for nanobiotechnological applications.
History
DepositionOct 18, 2018-
Header (metadata) releaseNov 14, 2018-
Map releaseAug 7, 2019-
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: 1.25
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6hxz
  • Surface level: 1.25
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6hxz
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0298.png

Downloads & links

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Map

FileDownload / File: emd_0298.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of Virus-Like Particle from Potato virus Y
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 360 pix.
= 381.96 Å		1.06 Å/pix.
x 360 pix.
= 381.96 Å		1.06 Å/pix.
x 360 pix.
= 381.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.25 / Movie #1: 1.25
Minimum - Maximum-6.7585998 - 9.995189999999999
Average (Standard dev.)0.00027839007 (±0.353567)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 381.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0611.0611.061
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z381.960381.960381.960
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-6.7599.9950.000

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Supplemental data

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Half map: Second half-map after 3D auto-refine in Relion.

Fileemd_0298_half_map_1.map
AnnotationSecond half-map after 3D auto-refine in Relion.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: First half-map after 3D auto-refine in Relion.

Fileemd_0298_half_map_2.map
AnnotationFirst half-map after 3D auto-refine in Relion.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Virus-like Particle based on Potato Virus Y

EntireName: Virus-like Particle based on Potato Virus Y
Components
  • Complex: Virus-like Particle based on Potato Virus Y
    • Complex: Coat protein of Potato Virus Y
      • Protein or peptide: Polyprotein

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Supramolecule #1: Virus-like Particle based on Potato Virus Y

SupramoleculeName: Virus-like Particle based on Potato Virus Y / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Recombinantly expressed coat protein self-assembles into virus-like particles.
Source (natural)Organism: Potato virus Y / Strain: NTN

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Supramolecule #2: Coat protein of Potato Virus Y

SupramoleculeName: Coat protein of Potato Virus Y / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Potato virus Y / Strain: NTN
Molecular weightTheoretical: 299 KDa

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Macromolecule #1: Polyprotein

MacromoleculeName: Polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Potato virus Y
Molecular weightTheoretical: 29.935797 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GNDTIDAGGS TKKDAKQEQG SIQPNLNKEK EKDVNVGTSG THTVPRIKAI TSKMRMPKSK GATVLNLEHL LEYAPQQIDI SNTRATQSQ FDTWYEAVQL AYDIGETEMP TVMNGLMVWC IENGTSPNIN GVWVMMDGDE QVEYPLKPIV ENAKPTLRQI M AHFSDVAE ...String:
GNDTIDAGGS TKKDAKQEQG SIQPNLNKEK EKDVNVGTSG THTVPRIKAI TSKMRMPKSK GATVLNLEHL LEYAPQQIDI SNTRATQSQ FDTWYEAVQL AYDIGETEMP TVMNGLMVWC IENGTSPNIN GVWVMMDGDE QVEYPLKPIV ENAKPTLRQI M AHFSDVAE AYIEMRNKKE PYMPRYGLVR NLRDGSLARY AFDFYEVTSR TPVRAREAHI QMKAAALKSA QSRLFGLDGG IS TQEENTE RHTTEDVSPS MHTLLGVKNM

UniProtKB: Genome polyprotein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration6.7 mg/mL
BufferpH: 7.4 / Component - Concentration: 12.0 mM / Component - Formula: PBS / Component - Name: Phosphate buffered saline / Details: 140 mM NaCl 2.7 mM KCl
GridModel: Quantifoil R2/1 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-16 / Number real images: 5344 / Average electron dose: 48.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 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

Final reconstructionApplied symmetry - Helical parameters - Δz: 42.65 Å
Applied symmetry - Helical parameters - Δ&Phi: 13.24 °
Applied symmetry - Helical parameters - Axial symmetry: C8 (8 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 148876
Segment selectionNumber selected: 244988 / Software - Name: EMAN2 / Software - details: e2helixboxer.py
Startup modelType of model: INSILICO MODEL
In silico model: Featureless cylinder constructed in Relion.
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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