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- EMDB-17053: Head-to-tail double ring assembly from truncated PVY coat protein -

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Basic information

Entry
Database: EMDB / ID: EMD-17053
TitleHead-to-tail double ring assembly from truncated PVY coat protein
Map datafinal trCP double ring cryoEM map after DeepEMhancer post-processing
Sample
  • Complex: truncated coat protein (dN49C40) with C-terminal His tag
    • Protein or peptide: Genome polyprotein
KeywordsH2T double ring / trCP / 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
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 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_17053.png

Downloads & links

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Map

FileDownload / File: emd_17053.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfinal trCP double ring cryoEM map after DeepEMhancer post-processing
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 350 pix.
= 332.5 Å		0.95 Å/pix.
x 350 pix.
= 332.5 Å		0.95 Å/pix.
x 350 pix.
= 332.5 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: 0.122
Minimum - Maximum-0.0018429302 - 1.9833119
Average (Standard dev.)0.0012201852 (±0.025349205)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 332.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17053_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: trCP double ring raw cryoEM map (C8)

Fileemd_17053_additional_1.map
AnnotationtrCP double ring raw cryoEM map (C8)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: trCP double ring half B cryoEM map

Fileemd_17053_half_map_1.map
AnnotationtrCP double ring half B cryoEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: trCP double ring half A cryoEM map

Fileemd_17053_half_map_2.map
AnnotationtrCP double ring 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 : truncated coat protein (dN49C40) with C-terminal His tag

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

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

SupramoleculeName: truncated coat protein (dN49C40) with C-terminal His tag
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The sample is a mixture of 2 types of filaments, double rings in a head-to-tail arrangement and their association products.
Source (natural)Organism: Potato virus Y strain NTN

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Macromolecule #1: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Potato virus Y strain NTN / Strain: NTN
Molecular weightTheoretical: 22.386461 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GITSKMRMPK SKGATVLNLE HLLEYAPQQI DISNTRATQS QFDTWYEAVQ LAYDIGETEM PTVMNGLMVW CIENGTSPNI NGVWVMMDG DEQVEYPLKP IVENAKPTLR QIMAHFSDVA EAYIEMRNKK EPYMPRYGLV RNLRDGSLAR YAFDFYEVTS R TPVRAREA ...String:
GITSKMRMPK SKGATVLNLE HLLEYAPQQI DISNTRATQS QFDTWYEAVQ LAYDIGETEM PTVMNGLMVW CIENGTSPNI NGVWVMMDG DEQVEYPLKP IVENAKPTLR QIMAHFSDVA EAYIEMRNKK EPYMPRYGLV RNLRDGSLAR YAFDFYEVTS R TPVRAREA HIQMKAAALK SENLYFQGLE HHHHHH

UniProtKB: Genome polyprotein

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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

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
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE
DetailsThe sample was polymorphic.

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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: 2862 / Average electron dose: 40.0 e/Å2

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Image processing

Particle selectionNumber selected: 1406546 / Details: Blob picker
Startup modelType of model: NONE
Details: Initial model was obtained by ab-initio reconstruction
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final reconstructionApplied symmetry - Point group: C8 (8 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Details: post-processing done with DeepEMHancer / Number images used: 174238
FSC plot (resolution estimation)

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