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- EMDB-0297: Potato virus Y -

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Basic information

Entry
Database: EMDB / ID: EMD-0297
TitlePotato virus Y
Map dataFinal cryo-EM map of Potato virus Y.
Sample
  • Virus: Potato virus Y
    • Complex: Coat protein
      • Protein or peptide: Coat protein
    • Complex: Viral RNA
      • RNA: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Keywordsplant virus / potyvirus / flexible filamentous particle / helical symmetry / VIRUS
Function / homologyPotyvirus coat protein / Potyvirus coat protein / viral capsid / Genome polyprotein
Function and homology information
Biological speciesPotato virus Y
Methodhelical reconstruction / cryo EM / Resolution: 3.4 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) releaseFeb 13, 2019-
Map releaseAug 7, 2019-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.132
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.132
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6hxx
  • Surface level: 0.132
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6hxx
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0297.png

Downloads & links

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Map

FileDownload / File: emd_0297.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal cryo-EM map of 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: 0.132 / Movie #1: 0.132
Minimum - Maximum-0.24860236 - 0.43469086
Average (Standard dev.)0.003057495 (±0.02427109)
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-0.2490.4350.003

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Supplemental data

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

Fileemd_0297_half_map_1.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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Half map: Second half-map after 3D auto-refine in Relion.

Fileemd_0297_half_map_2.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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Sample components

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Entire : Potato virus Y

EntireName: Potato virus Y
Components
  • Virus: Potato virus Y
    • Complex: Coat protein
      • Protein or peptide: Coat protein
    • Complex: Viral RNA
      • RNA: RNA (5'-R(P*UP*UP*UP*UP*U)-3')

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Supramolecule #1: Potato virus Y

SupramoleculeName: Potato virus Y / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Potato virus Y / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Solanum tuberosum (potato)

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Supramolecule #2: Coat protein

SupramoleculeName: Coat protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: Approximately 2000 copies of PVY coat protein assemble around viral ssRNA to form the virion.
Source (natural)Organism: Potato virus Y / Strain: NTN
Molecular weightTheoretical: 299 KDa

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Supramolecule #3: Viral RNA

SupramoleculeName: Viral RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Details: Viral genome consists of positive-sense single stranded RNA.
Source (natural)Organism: Potato virus Y / Strain: NTN

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Macromolecule #1: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 35 / Enantiomer: LEVO
Source (natural)Organism: Potato virus Y
Molecular weightTheoretical: 29.935797 KDa
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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Macromolecule #2: RNA (5'-R(P*UP*UP*UP*UP*U)-3')

MacromoleculeName: RNA (5'-R(P*UP*UP*UP*UP*U)-3') / type: rna / ID: 2
Details: Due to helical averaging during cryo-EM data processing, all nucleotides were assigned the uracil base.
Number of copies: 35
Source (natural)Organism: Potato virus Y
Molecular weightTheoretical: 1.485872 KDa
SequenceString:
UUUUU

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration0.9 mg/mL
BufferpH: 8 / Component - Concentration: 5.0 mM / Component - Formula: B4Na2O7 / Component - Name: disodium tetraborate
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: 726 / 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: 3.95 Å
Applied symmetry - Helical parameters - Δ&Phi: -40.95 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 162213
Segment selectionNumber selected: 215123
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5fn1

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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