+Open data
-Basic information
Entry | Database: PDB / ID: 7og6 | ||||||
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Title | Structure of Alternanthera Mosaic VLP by cryoEM | ||||||
Components |
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Keywords | VIRUS LIKE PARTICLE / Potexvirus / VLP. | ||||||
Function / homology | Potexviruses and carlaviruses coat protein signature. / Potex/carlavirus coat protein / Viral coat protein / viral capsid / ribonucleoprotein complex / structural molecule activity / RNA / Coat protein Function and homology information | ||||||
Biological species | Alternanthera mosaic virus | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Byrne, M.J. / Ranson, N.A. / Lomonossoff, G.P. / Thuenemann, E.C. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Viruses / Year: 2021 Title: A Replicating Viral Vector Greatly Enhances Accumulation of Helical Virus-Like Particles in Plants. Authors: Eva C Thuenemann / Matthew J Byrne / Hadrien Peyret / Keith Saunders / Roger Castells-Graells / Inmaculada Ferriol / Mattia Santoni / John F C Steele / Neil A Ranson / Linda Avesani / Juan ...Authors: Eva C Thuenemann / Matthew J Byrne / Hadrien Peyret / Keith Saunders / Roger Castells-Graells / Inmaculada Ferriol / Mattia Santoni / John F C Steele / Neil A Ranson / Linda Avesani / Juan Jose Lopez-Moya / George P Lomonossoff / Abstract: The production of plant helical virus-like particles (VLPs) via plant-based expression has been problematic with previous studies suggesting that an RNA scaffold may be necessary for their efficient ...The production of plant helical virus-like particles (VLPs) via plant-based expression has been problematic with previous studies suggesting that an RNA scaffold may be necessary for their efficient production. To examine this, we compared the accumulation of VLPs from two potexviruses, papaya mosaic virus and alternanthera mosaic virus (AltMV), when the coat proteins were expressed from a replicating potato virus X- based vector (pEff) and a non-replicating vector (pEAQ-). Significantly greater quantities of VLPs could be purified when pEff was used. The pEff system was also very efficient at producing VLPs of helical viruses from different virus families. Examination of the RNA content of AltMV and tobacco mosaic virus VLPs produced from pEff revealed the presence of vector-derived RNA sequences, suggesting that the replicating RNA acts as a scaffold for VLP assembly. Cryo-EM analysis of the AltMV VLPs showed they had a structure very similar to that of authentic potexvirus particles. Thus, we conclude that vectors generating replicating forms of RNA, such as pEff, are very efficient for producing helical VLPs. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7og6.cif.gz | 47.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7og6.ent.gz | 31.7 KB | Display | PDB format |
PDBx/mmJSON format | 7og6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7og6_validation.pdf.gz | 936.1 KB | Display | wwPDB validaton report |
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Full document | 7og6_full_validation.pdf.gz | 937.4 KB | Display | |
Data in XML | 7og6_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 7og6_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/7og6 ftp://data.pdbj.org/pub/pdb/validation_reports/og/7og6 | HTTPS FTP |
-Related structure data
Related structure data | 12879MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 22243.895 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alternanthera mosaic virus / Gene: CP / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q52Z61 |
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#2: RNA chain | Mass: 1485.872 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alternanthera mosaic virus / Production host: Nicotiana benthamiana (plant) |
-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: Alternanthera mosaic virus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Alternanthera mosaic virus |
Source (recombinant) | Organism: Nicotiana benthamiana (plant) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE |
Buffer solution | pH: 8 / Details: 10 mM Tris-HCl, pH 8.0 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.11 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: RELION / Version: 3.1 / Category: 3D reconstruction | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 41.11 ° / Axial rise/subunit: 3.959 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32018 / Symmetry type: HELICAL | ||||||||||||||||||||||||
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