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- PDB-8opl: Virus-like Particle based on PVY coat protein with T43C and D136C... -

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Basic information

Entry
Database: PDB / ID: 8opl
TitleVirus-like Particle based on PVY coat protein with T43C and D136C mutation with helical architecture encapsidating ssRNA
Components
  • Genome polyprotein (Fragment)
  • RNA (5'-R(P*UP*UP*UP*UP*U)-3')
KeywordsVIRUS LIKE PARTICLE / helical / VLP / ssRNA / Potyvirus / PVY
Function / homologyPotyvirus coat protein / Potyvirus coat protein / viral capsid / RNA / Genome polyprotein
Function and homology information
Biological speciesPotato virus Y strain NTN
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.41 Å
AuthorsKavcic, L. / Kezar, A. / Podobnik, M.
Funding support Slovenia, 2items
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, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Aa: Genome polyprotein (Fragment)
Ab: Genome polyprotein (Fragment)
Ac: Genome polyprotein (Fragment)
Ad: Genome polyprotein (Fragment)
Ae: Genome polyprotein (Fragment)
Af: Genome polyprotein (Fragment)
Ag: Genome polyprotein (Fragment)
Ah: Genome polyprotein (Fragment)
Ai: Genome polyprotein (Fragment)
Aj: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Ak: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Al: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Am: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
An: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Ao: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Ap: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Aq: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Ar: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
As: Genome polyprotein (Fragment)
At: Genome polyprotein (Fragment)
Au: Genome polyprotein (Fragment)
Av: Genome polyprotein (Fragment)
Aw: Genome polyprotein (Fragment)
Ax: Genome polyprotein (Fragment)
Ay: Genome polyprotein (Fragment)
Az: Genome polyprotein (Fragment)
Ba: Genome polyprotein (Fragment)
Bb: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bc: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bd: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Be: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bf: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bg: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bh: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bi: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bj: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bk: Genome polyprotein (Fragment)
Bl: Genome polyprotein (Fragment)
Bm: Genome polyprotein (Fragment)
Bn: Genome polyprotein (Fragment)
Bo: Genome polyprotein (Fragment)
Bp: Genome polyprotein (Fragment)
Bq: Genome polyprotein (Fragment)
Br: Genome polyprotein (Fragment)
Bs: Genome polyprotein (Fragment)
Bt: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bu: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bv: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bw: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bx: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
By: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bz: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Ca: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Cb: RNA (5'-R(P*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)848,11854
Polymers848,11854
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Genome polyprotein (Fragment)


Mass: 29925.891 Da / Num. of mol.: 27
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Potato virus Y strain NTN / Plasmid: pT7-7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7DGZ0
#2: RNA chain ...
RNA (5'-R(P*UP*UP*UP*UP*U)-3')


Mass: 1485.872 Da / Num. of mol.: 27
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Potato virus Y strain NTN / Plasmid: pT7-7 / Production host: Escherichia coli BL21(DE3) (bacteria)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Virus-like particles from PVY coat protein with T43C and D136C mutations
Type: COMPLEX
Details: Monomorphic filaments with helical architecture and encapsidated RNA
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Potato virus Y strain NTN
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL221 (DE3) / Plasmid: pT7-7
Buffer solutionpH: 7.4
Details: 1.8 mM KH2PO4, 10.1 mM Na2HPO4, 140 mM NaCl, 2.7 mM KCl, pH 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 461

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
4CTFFIND4.1CTF correction
7Cootmodel fitting
9PHENIX1.2model refinement
10RELION4.1initial Euler assignment
13cryoSPARC4.13D reconstruction
CTF correctionDetails: CTFFIND-4.1 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -40.997 ° / Axial rise/subunit: 4.005 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 195881 / Details: CrYOLO picking based on pre-trained neural network
3D reconstructionResolution: 2.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 141112
Details: Final reconstruction was performed in CryoSPARC after Bayesian polishing of particles in RELION.
Symmetry type: HELICAL

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