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- EMDB-17050: Virus-like Particle based on PVY coat protein with dC40 deletion ... -

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Basic information

Entry
Database: EMDB / ID: EMD-17050
TitleVirus-like Particle based on PVY coat protein with dC40 deletion with helical architecture encapsidating ssRNA
Map datafinal VLPdC40:hRNA sharp symmetric cryoEM map after Phenix density modification
Sample
  • Complex: Virus-like particle from dC40 coat protein
    • Protein or peptide: Genome polyprotein (Fragment)
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Keywordshelical / dC40 / VLP / ssRNA / Potyvirus / PVY / VIRUS LIKE PARTICLE
Function / homologyPotyvirus coat protein / Potyvirus coat protein / viral capsid / Genome polyprotein
Function and homology information
Biological speciesPotato virus Y strain NTN
Methodhelical reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsKavcic L / Kezar A / Podobnik M
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: Commun Chem / Year: 2024
Title: From structural polymorphism to structural metamorphosis of the coat protein of flexuous filamentous potato virus Y.
Authors: Luka Kavčič / Andreja Kežar / Neža Koritnik / Magda Tušek Žnidarič / Tajda Klobučar / Žiga Vičič / Franci Merzel / Ellie Holden / Justin L P Benesch / Marjetka Podobnik /
Abstract: The structural diversity and tunability of the capsid proteins (CPs) of various icosahedral and rod-shaped viruses have been well studied and exploited in the development of smart hybrid ...The structural diversity and tunability of the capsid proteins (CPs) of various icosahedral and rod-shaped viruses have been well studied and exploited in the development of smart hybrid nanoparticles. However, the potential of CPs of the wide-spread flexuous filamentous plant viruses remains to be explored. Here, we show that we can control the shape, size, RNA encapsidation ability, symmetry, stability and surface functionalization of nanoparticles through structure-based design of CP from potato virus Y (PVY). We provide high-resolution insight into CP-based self-assemblies, ranging from large polymorphic or monomorphic filaments to smaller annular, cubic or spherical particles. Furthermore, we show that we can prevent CP self-assembly in bacteria by fusion with a cleavable protein, enabling controlled nanoparticle formation in vitro. Understanding the remarkable structural diversity of PVY CP not only provides possibilities for the production of biodegradable nanoparticles, but may also advance future studies of CP's polymorphism in a biological context.
History
DepositionApr 7, 2023-
Header (metadata) releaseJan 24, 2024-
Map releaseJan 24, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17050.png

Downloads & links

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Map

FileDownload / File: emd_17050.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfinal VLPdC40:hRNA sharp symmetric cryoEM map after Phenix density modification
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 318.9 Å		1.06 Å/pix.
x 300 pix.
= 318.9 Å		1.06 Å/pix.
x 300 pix.
= 318.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.063 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.237
Minimum - Maximum-0.54273915 - 1.0803921
Average (Standard dev.)0.0007479693 (±0.058665548)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 318.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17050_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: VLPdC40:hRNA raw cryoEM map

Fileemd_17050_additional_1.map
AnnotationVLPdC40:hRNA raw cryoEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: VLPdC40:hRNA cryoEM map after imposing helical symmetry

Fileemd_17050_additional_2.map
AnnotationVLPdC40:hRNA cryoEM map after imposing helical symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: VLPdC40:hRNA unfiltered half cryoEM map 1

Fileemd_17050_half_map_1.map
AnnotationVLPdC40:hRNA unfiltered half cryoEM map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: VLPdC40:hRNA unfiltered half cryoEM map 2

Fileemd_17050_half_map_2.map
AnnotationVLPdC40:hRNA unfiltered half cryoEM map 2
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 from dC40 coat protein

EntireName: Virus-like particle from dC40 coat protein
Components
  • Complex: Virus-like particle from dC40 coat protein
    • Protein or peptide: Genome polyprotein (Fragment)
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*U)-3')

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Supramolecule #1: Virus-like particle from dC40 coat protein

SupramoleculeName: Virus-like particle from dC40 coat protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: The sample contains 2 forms of filaments.
Source (natural)Organism: Potato virus Y strain NTN

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Macromolecule #1: Genome polyprotein (Fragment)

MacromoleculeName: Genome polyprotein (Fragment) / type: protein_or_peptide / ID: 1
Details: Due to flexibility, structural model could only be built from H42 to S227.
Number of copies: 21 / Enantiomer: LEVO
Source (natural)Organism: Potato virus Y strain NTN / Strain: NTN
Molecular weightTheoretical: 25.561 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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 QMKAAALKS

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 / Number of copies: 21
Source (natural)Organism: Potato virus Y strain NTN
Molecular weightTheoretical: 1.485872 KDa
SequenceString:
UUUUU

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
Details: 1.8 mM KH2PO4, 10.1 mM Na2HPO4, 140 mM NaCl, 2.7 mM KCl, pH 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number real images: 4805 / Average exposure time: 1.02 sec. / Average electron dose: 84.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.3 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 75000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.05 Å
Applied symmetry - Helical parameters - Δ&Phi: -41.05 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Software:
Namedetails
RELION
PHENIXDensity modification

Details: Final cryoEM map was obtained by Phenix density modification.
Number images used: 152296
Segment selectionNumber selected: 2966850 / Software - Name: crYOLO
Details: CrYOLO filament picking based on pre-trained neural network model
Startup modelType of model: NONE / Details: Ab-initio model in cryoSPARC
Final angle assignmentType: NOT APPLICABLE

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