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- EMDB-17073: Virus-like Particle based on PVY coat protein with D136C mutation... -

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Basic information

Entry
Database: EMDB / ID: EMD-17073
TitleVirus-like Particle based on PVY coat protein with D136C mutation with helical architecture encapsidating ssRNA
Map dataD136C VLPhRNA sharp symmetric cryoEM map
Sample
  • Complex: Virus-like particle from PVY coat protein with D136C mutation
    • Protein or peptide: coat protein with D136C mutation
Keywordshelical / VLP / ssRNA / Potyvirus / PVY / VIRUS LIKE PARTICLE
Biological speciesPotato virus Y strain NTN
Methodhelical reconstruction / cryo EM / Resolution: 3.46 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_17073.png

Downloads & links

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Map

FileDownload / File: emd_17073.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationD136C VLPhRNA sharp symmetric cryoEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 300 pix.
= 292.8 Å		0.98 Å/pix.
x 300 pix.
= 292.8 Å		0.98 Å/pix.
x 300 pix.
= 292.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.976 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.831
Minimum - Maximum-1.9900415 - 2.5461924
Average (Standard dev.)0.02377681 (±0.19098431)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 292.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17073_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: D136C VLPhRNA raw cryoEM map

Fileemd_17073_additional_1.map
AnnotationD136C VLPhRNA raw cryoEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: D136C VLPhRNA half B cryoEM map

Fileemd_17073_half_map_1.map
AnnotationD136C VLPhRNA half B cryoEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: D136C VLPhRNA half A cryoEM map

Fileemd_17073_half_map_2.map
AnnotationD136C VLPhRNA half A 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 particle from PVY coat protein with D136C mutation

EntireName: Virus-like particle from PVY coat protein with D136C mutation
Components
  • Complex: Virus-like particle from PVY coat protein with D136C mutation
    • Protein or peptide: coat protein with D136C mutation

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Supramolecule #1: Virus-like particle from PVY coat protein with D136C mutation

SupramoleculeName: Virus-like particle from PVY coat protein with D136C mutation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Architecturally homogenous VLPs (VLPh+RNA)
Source (natural)Organism: Potato virus Y strain NTN

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Macromolecule #1: coat protein with D136C mutation

MacromoleculeName: coat protein with D136C mutation / 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 EKDVNVGTSG THTVPRIKAI TSKMRMPKSK GATVLNLEHL LEYAPQQIDI SNTRATQSQF DTWYEAVQLA YDIGETEMPT VMNGLMVWCI ENGTSPNING VWVMMCGDEQ VEYPLKPIVE NAKPTLRQIM AHFSDVAEAY ...String:
GNDTIDAGGS TKKDAKQEQG SIQPNLNKEK EKDVNVGTSG THTVPRIKAI TSKMRMPKSK GATVLNLEHL LEYAPQQIDI SNTRATQSQF DTWYEAVQLA YDIGETEMPT VMNGLMVWCI ENGTSPNING VWVMMCGDEQ 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
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 150000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 555 / Average electron dose: 40.0 e/Å2

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Image processing

Segment selectionNumber selected: 93351 / Software - Name: cryoSPARC / Details: cryoSPARC Filament tracer
Startup modelType of model: NONE / Details: Ab-initio reconstruction in cryoSPARC
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Helical parameters - Δz: 4.08 Å
Applied symmetry - Helical parameters - Δ&Phi: -40.961 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 20432
FSC plot (resolution estimation)

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