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- EMDB-17065: Cubic assembly from truncated PVY coat protein with K176C mutatio... -

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Basic information

Entry
Database: EMDB / ID: EMD-17065
TitleCubic assembly from truncated PVY coat protein with K176C mutation and removed His tag
Map datatrCPCHisX-K176C cubic particle sharp cryoEM map
Sample
  • Complex: truncated coat protein (dN49C40) with cleaved C-terminal His tag and K176C mutation
    • Protein or peptide: truncated coat protein (dN49C40) with cleaved C-terminal His tag and K176C mutation
Keywordscubes / trCPnoHis / K176C / Potyvirus / PVY / VIRUS LIKE PARTICLE
Biological speciesPotato virus Y strain NTN
Methodsingle particle reconstruction / cryo EM / Resolution: 4.16 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_17065.png

Downloads & links

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Map

FileDownload / File: emd_17065.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationtrCPCHisX-K176C cubic particle sharp cryoEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 400 pix.
= 390.4 Å		0.98 Å/pix.
x 400 pix.
= 390.4 Å		0.98 Å/pix.
x 400 pix.
= 390.4 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: 0.254
Minimum - Maximum-1.0254169 - 1.6103401
Average (Standard dev.)-0.0010315261 (±0.05865484)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 390.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17065_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: trCPCHisX-K176C cubic particle raw cryoEM map

Fileemd_17065_additional_1.map
AnnotationtrCPCHisX-K176C cubic particle raw cryoEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: trCPCHisX-K176C cubic particle half A cryoEM map

Fileemd_17065_half_map_1.map
AnnotationtrCPCHisX-K176C cubic particle half A cryoEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: trCPCHisX-K176C cubic particle half B cryoEM map

Fileemd_17065_half_map_2.map
AnnotationtrCPCHisX-K176C cubic particle 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 cleaved C-terminal His tag ...

EntireName: truncated coat protein (dN49C40) with cleaved C-terminal His tag and K176C mutation
Components
  • Complex: truncated coat protein (dN49C40) with cleaved C-terminal His tag and K176C mutation
    • Protein or peptide: truncated coat protein (dN49C40) with cleaved C-terminal His tag and K176C mutation

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

SupramoleculeName: truncated coat protein (dN49C40) with cleaved C-terminal His tag and K176C mutation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: structurally homogenous cubic particle
Source (natural)Organism: Potato virus Y strain NTN
Molecular weightTheoretical: 1.265 MDa

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

MacromoleculeName: truncated coat protein (dN49C40) with cleaved C-terminal His tag and K176C 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 VENAKPTLRQ IMAHFSDVAE AYIEMRNCKE PYMPRYGLVR NLRDGSLARY AFDFYEVTSR TPVRAREAHI QMKAAALKSE NLYFQ

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4 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
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
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 1970 / Average electron dose: 40.0 e/Å2

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Image processing

Particle selectionNumber selected: 412940
Startup modelType of model: NONE
Details: Initial model was obtained by ab-initio reconstruction
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 4.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 84675
FSC plot (resolution estimation)

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