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Yorodumi- PDB-8opd: Virus-like Particle based on PVY coat protein with dC40 deletion ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8opd | ||||||||||||
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Title | Virus-like Particle based on PVY coat protein with dC40 deletion with stacked-ring architecture | ||||||||||||
Components | Genome polyprotein (Fragment) | ||||||||||||
Keywords | VIRUS LIKE PARTICLE / stacked-ring / dC40 / VLP / Potyvirus / PVY | ||||||||||||
Function / homology | Potyvirus coat protein / Potyvirus coat protein / viral capsid / Genome polyprotein Function and homology information | ||||||||||||
Biological species | Potato virus Y strain NTN | ||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
Authors | Kavcic, L. / Kezar, A. / Podobnik, M. | ||||||||||||
Funding support | Slovenia, Czech Republic, 3items
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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 | 8opd.cif.gz | 743.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8opd.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8opd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8opd_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8opd_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8opd_validation.xml.gz | 107.3 KB | Display | |
Data in CIF | 8opd_validation.cif.gz | 141.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/8opd ftp://data.pdbj.org/pub/pdb/validation_reports/op/8opd | HTTPS FTP |
-Related structure data
Related structure data | 17049MC 8opaC 8opbC 8opcC 8opeC 8opfC 8opgC 8ophC 8opjC 8opkC 8oplC C: citing same article (ref.) M: map data used to model this data |
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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: 25561.000 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Details: Due to flexibility, structural model could only be built from T41 to K221. Source: (gene. exp.) Potato virus Y strain NTN / Strain: NTN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A7DJG2 |
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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 particle from dC40 coat protein / Type: COMPLEX / Details: The sample contains 2 forms of filaments. / 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: BL21 (DE3) |
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
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 1300 nm / Nominal defocus min: 400 nm |
Image recording | Average exposure time: 1.02 sec. / Electron dose: 84 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 4805 |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 15.04 ° / Axial rise/subunit: 43.29 Å / Axial symmetry: C8 | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2966850 Details: CrYOLO filament picking based on pre-trained neural network model | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 399617 Details: Final cryoEM map was obtained by Phenix density modification. Symmetry type: HELICAL |