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Yorodumi- PDB-7pe1: Cryo-EM structure of BMV-derived VLP expressed in E. coli and ass... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pe1 | ||||||
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Title | Cryo-EM structure of BMV-derived VLP expressed in E. coli and assembled in the presence of tRNA (tVLP) | ||||||
Components | Coat protein | ||||||
Keywords | VIRUS LIKE PARTICLE / BMV / brome mosaic virus / capsid proteins | ||||||
Function / homology | Bromovirus coat protein / Bromovirus coat protein / viral capsid / structural molecule activity / Coat protein Function and homology information | ||||||
Biological species | Brome mosaic virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Ruszkowski, M. / Strugala, A. / Indyka, P. / Urbanowicz, A. | ||||||
Funding support | 1items
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Citation | Journal: Nanoscale / Year: 2022 Title: Cryo-EM reconstructions of BMV-derived virus-like particles reveal assembly defects in the icosahedral lattice structure. Authors: Milosz Ruszkowski / Aleksander Strugala / Paulina Indyka / Guillaume Tresset / Marek Figlerowicz / Anna Urbanowicz / Abstract: The increasing interest in virus-like particles (VLPs) has been reflected by the growing number of studies on their assembly and application. However, the formation of complete VLPs is a complex ...The increasing interest in virus-like particles (VLPs) has been reflected by the growing number of studies on their assembly and application. However, the formation of complete VLPs is a complex phenomenon, making it difficult to rationally design VLPs with desired features . In this paper, we describe VLPs assembled from the recombinant capsid protein of brome mosaic virus (BMV). The analysis of VLPs was performed by Cryo-EM reconstructions and allowed us to visualize a few classes of VLPs, giving insight into the VLP self-assembly process. Apart from the mature icosahedral VLP practically identical with native virions, we describe putative VLP intermediates displaying non-icosahedral arrangements of capsomers, proposed to occur before the final disorder-order transition stage of icosahedral VLP assembly. Some of the described VLP classes show a lack of protein shell continuity, possibly resulting from too strong interaction with the cargo (in this case tRNA) with the capsid protein. We believe that our results are a useful prerequisite for the rational design of VLPs in the future and lead the way to the effective production of modified 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 | 7pe1.cif.gz | 4.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7pe1.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7pe1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pe1_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 7pe1_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 7pe1_validation.xml.gz | 623 KB | Display | |
Data in CIF | 7pe1_validation.cif.gz | 955.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/7pe1 ftp://data.pdbj.org/pub/pdb/validation_reports/pe/7pe1 | HTTPS FTP |
-Related structure data
Related structure data | 13344MC 7pe2C 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: 20568.693 Da / Num. of mol.: 180 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brome mosaic virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QCJ1 #2: Water | ChemComp-HOH / | |
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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: Brome mosaic virus / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Brome mosaic virus |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE |
Buffer solution | pH: 4.8 Details: 25 mM NaOAc pH 4.8, 5 mM MgCl2, 25 mM NaCl, 10 mM KCl |
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: 300 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / 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 / Calibrated magnification: 105000 X / Calibrated defocus min: 900 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 17955 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1419349 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24812 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6VOC Accession code: 6VOC / Source name: PDB / Type: experimental model |