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- EMDB-17070: Virus-like Particle based on PVY coat protein with S39C and E72C ... -

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Basic information

Entry
Database: EMDB / ID: EMD-17070
TitleVirus-like Particle based on PVY coat protein with S39C and E72C mutation with stacked-ring architecture
Map dataS39C E72C:VLPr sharp cryoEM map
Sample
  • Complex: Virus-like particles from PVY coat protein with S39C and E72C mutations
    • Protein or peptide: coat protein with S39C and E72C mutations
Keywordsstacked-ring / disulfide-staple / VLP / Potyvirus / PVY / VIRUS LIKE PARTICLE
Biological speciesPotato virus Y strain NTN
Methodhelical reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsKavcic L / Kezar A / Podobnik M
Funding support Slovenia, 2 items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0391 Slovenia
Slovenian Research AgencyJ7-7248 Slovenia
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_17070.png

Downloads & links

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Map

FileDownload / File: emd_17070.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationS39C E72C:VLPr sharp cryoEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.309
Minimum - Maximum-1.728918 - 2.9871392
Average (Standard dev.)0.008631752 (±0.12781306)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 285.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17070_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: S39C E72C:VLPr raw cryoEM map

Fileemd_17070_additional_1.map
AnnotationS39C E72C:VLPr raw cryoEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: S39C E72C:VLPr half A cryoEM map

Fileemd_17070_half_map_1.map
AnnotationS39C E72C:VLPr half A cryoEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: S39C E72C:VLPr half B cryoEM map

Fileemd_17070_half_map_2.map
AnnotationS39C E72C:VLPr half B cryoEM map
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 particles from PVY coat protein with S39C and E72C mut...

EntireName: Virus-like particles from PVY coat protein with S39C and E72C mutations
Components
  • Complex: Virus-like particles from PVY coat protein with S39C and E72C mutations
    • Protein or peptide: coat protein with S39C and E72C mutations

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Supramolecule #1: Virus-like particles from PVY coat protein with S39C and E72C mut...

SupramoleculeName: Virus-like particles from PVY coat protein with S39C and E72C mutations
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Potato virus Y strain NTN

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Macromolecule #1: coat protein with S39C and E72C mutations

MacromoleculeName: coat protein with S39C and E72C mutations / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Potato virus Y strain NTN / Strain: NTN
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GNDTIDAGGS TKKDAKQEQG SIQPNLNKEK EKDVNVGTCG THTVPRIKAI TSKMRMPKSK GATVLNLEHL LCYAPQQIDI SNTRATQSQF DTWYEAVQLA YDIGETEMPT VMNGLMVWCI ENGTSPNING VWVMMDGDEQ VEYPLKPIVE NAKPTLRQIM AHFSDVAEAY ...String:
GNDTIDAGGS TKKDAKQEQG SIQPNLNKEK EKDVNVGTCG THTVPRIKAI TSKMRMPKSK GATVLNLEHL LCYAPQQIDI SNTRATQSQF DTWYEAVQLA YDIGETEMPT VMNGLMVWCI ENGTSPNING VWVMMDGDEQ VEYPLKPIVE NAKPTLRQIM AHFSDVAEAY IEMRNKKEPY MPRYGLVRNL RDGSLARYAF DFYEVTSRTP VRAREAHIQM KAAALKSAQS RLFGLDGGIS TQEENTERHT TEDVSPSMHT LLGVKNM

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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 / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 2022 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 150000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 43.22 Å
Applied symmetry - Helical parameters - Δ&Phi: 13.160 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 164605
Segment selectionNumber selected: 380456 / Software - Name: crYOLO / Details: CrYOLO filament picker
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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