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Yorodumi- PDB-8oph: Head-to-tail double ring assembly from truncated PVY coat protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 8oph | |||||||||
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Title | Head-to-tail double ring assembly from truncated PVY coat protein | |||||||||
Components | Genome polyprotein | |||||||||
Keywords | VIRUS LIKE PARTICLE / H2T double ring / trCP / 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 / single particle reconstruction / cryo EM / Resolution: 2.93 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 | 8oph.cif.gz | 522.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oph.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8oph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8oph_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8oph_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8oph_validation.xml.gz | 78.6 KB | Display | |
Data in CIF | 8oph_validation.cif.gz | 105.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/8oph ftp://data.pdbj.org/pub/pdb/validation_reports/op/8oph | HTTPS FTP |
-Related structure data
Related structure data | 17053MC 8opaC 8opbC 8opcC 8opdC 8opeC 8opfC 8opgC 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: 22386.461 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Potato virus Y strain NTN / Strain: NTN / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A7DIZ4 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: truncated coat protein (dN49C40) with C-terminal His tag Type: COMPLEX Details: The sample is a mixture of 2 types of filaments, double rings in a head-to-tail arrangement and their association products. 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) / Plasmid: pET28a |
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.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The sample was polymorphic. |
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 |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 2862 |
-Processing
EM software |
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CTF correction | Details: patchCTF correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1406546 / Details: Blob picker | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C8 (8 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 174238 / Details: post-processing done with DeepEMHancer / Symmetry type: POINT |