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- EMDB-17058: Helical assembly from truncated PVY coat protein with K153E mutation -

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Basic information

Entry
Database: EMDB / ID: EMD-17058
TitleHelical assembly from truncated PVY coat protein with K153E mutation
Map datatrCPK153E helical filament sharp symmetric cryoEM map
Sample
  • Complex: truncated coat protein (dN49C40) with C-terminal His tag and K153E mutation
    • Protein or peptide: truncated coat protein (dN49C40) with C-terminal His tag and K153E mutation
Keywordshelical / RNA-free / trCP / K153E / Potyvirus / PVY / VIRUS LIKE PARTICLE
Biological speciesPotato virus Y strain NTN
Methodhelical reconstruction / cryo EM / Resolution: 3.41 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_17058.png

Downloads & links

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Map

FileDownload / File: emd_17058.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationtrCPK153E helical filament 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: 0.867
Minimum - Maximum-1.9204196 - 3.6020308
Average (Standard dev.)0.016684085 (±0.1844877)
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_17058_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: trCPK153E helical filament raw cryoEM map

Fileemd_17058_additional_1.map
AnnotationtrCPK153E helical filament raw cryoEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: trCPK153E helical filament half A cryoEM map

Fileemd_17058_half_map_1.map
AnnotationtrCPK153E helical filament half A cryoEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: trCPK153E helical filament half B cryoEM map

Fileemd_17058_half_map_2.map
AnnotationtrCPK153E helical filament 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 : truncated coat protein (dN49C40) with C-terminal His tag and K153...

EntireName: truncated coat protein (dN49C40) with C-terminal His tag and K153E mutation
Components
  • Complex: truncated coat protein (dN49C40) with C-terminal His tag and K153E mutation
    • Protein or peptide: truncated coat protein (dN49C40) with C-terminal His tag and K153E mutation

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Supramolecule #1: truncated coat protein (dN49C40) with C-terminal His tag and K153...

SupramoleculeName: truncated coat protein (dN49C40) with C-terminal His tag and K153E mutation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Potato virus Y strain NTN

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Macromolecule #1: truncated coat protein (dN49C40) with C-terminal His tag and K153...

MacromoleculeName: truncated coat protein (dN49C40) with C-terminal His tag and K153E 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: GITSKMRMPK SKGATVLNLE HLLEYAPQQI DISNTRATQS QFDTWYEAVQ LAYDIGETEM PTVMNGLMVW CIENGTSPNI NGVWVMMDGD EQVEYPLKPI VENAEPTLRQ IMAHFSDVAE AYIEMRNKKE PYMPRYGLVR NLRDGSLARY AFDFYEVTSR TPVRAREAHI ...String:
GITSKMRMPK SKGATVLNLE HLLEYAPQQI DISNTRATQS QFDTWYEAVQ LAYDIGETEM PTVMNGLMVW CIENGTSPNI NGVWVMMDGD EQVEYPLKPI VENAEPTLRQ IMAHFSDVAE AYIEMRNKKE PYMPRYGLVR NLRDGSLARY AFDFYEVTSR TPVRAREAHI QMKAAALKSE NLYFQGLEHH HHHH

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 7.4
Details: 1.8 mM KH2PO4, 10.1 mM Na2HPO4, 140 mM NaCl, 2.7 mM KCl, pH 7.4
VitrificationCryogen name: ETHANE
DetailsThe sample was polymorphic.

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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: 399 / 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

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.06 Å
Applied symmetry - Helical parameters - Δ&Phi: -44.45 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 21629
Segment selectionNumber selected: 23662 / Software - Name: cryoSPARC / Details: Filament tracer
Startup modelType of model: NONE
Details: Initial model was obtained by ab-initio reconstruction
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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