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Yorodumi- PDB-8opl: Virus-like Particle based on PVY coat protein with T43C and D136C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8opl | |||||||||
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Title | Virus-like Particle based on PVY coat protein with T43C and D136C mutation with helical architecture encapsidating ssRNA | |||||||||
Components |
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Keywords | VIRUS LIKE PARTICLE / helical / VLP / ssRNA / Potyvirus / PVY | |||||||||
Function / homology | Potyvirus coat protein / Potyvirus coat protein / viral capsid / RNA / Genome polyprotein Function and homology information | |||||||||
Biological species | Potato virus Y strain NTN | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.41 Å | |||||||||
Authors | Kavcic, L. / Kezar, A. / Podobnik, M. | |||||||||
Funding support | Slovenia, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8opl.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8opl.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8opl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8opl_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8opl_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8opl_validation.xml.gz | 146.1 KB | Display | |
Data in CIF | 8opl_validation.cif.gz | 202.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/8opl ftp://data.pdbj.org/pub/pdb/validation_reports/op/8opl | HTTPS FTP |
-Related structure data
Related structure data | 17072MC 8opaC 8opbC 8opcC 8opdC 8opeC 8opfC 8opgC 8ophC 8opjC 8opkC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: 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 |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Potato virus Y strain NTN |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL221 (DE3) / Plasmid: pT7-7 |
Buffer solution | pH: 7.4 Details: 1.8 mM KH2PO4, 10.1 mM Na2HPO4, 140 mM NaCl, 2.7 mM KCl, pH 7.4 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 800 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 461 |
-Processing
EM software |
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CTF correction | Details: CTFFIND-4.1 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -40.997 ° / Axial rise/subunit: 4.005 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 195881 / Details: CrYOLO picking based on pre-trained neural network | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 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 |