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Yorodumi- EMDB-13345: Cryo-EM structure of BMV-derived VLP expressed in E. coli (eVLP) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13345 | |||||||||
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Title | Cryo-EM structure of BMV-derived VLP expressed in E. coli (eVLP) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | BMV / brome mosaic virus / capsid proteins / VIRUS LIKE PARTICLE | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Ruszkowski M / Strugala A | |||||||||
Funding support | 1 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13345.map.gz | 474.1 MB | EMDB map data format | |
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Header (meta data) | emd-13345-v30.xml emd-13345.xml | 11.8 KB 11.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13345_fsc.xml | 18.2 KB | Display | FSC data file |
Images | emd_13345.png | 255.3 KB | ||
Filedesc metadata | emd-13345.cif.gz | 5.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13345 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13345 | HTTPS FTP |
-Validation report
Summary document | emd_13345_validation.pdf.gz | 802.5 KB | Display | EMDB validaton report |
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Full document | emd_13345_full_validation.pdf.gz | 802 KB | Display | |
Data in XML | emd_13345_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | emd_13345_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13345 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13345 | HTTPS FTP |
-Related structure data
Related structure data | 7pe2MC 7pe1C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13345.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Brome mosaic virus
Entire | Name: Brome mosaic virus |
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Components |
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-Supramolecule #1: Brome mosaic virus
Supramolecule | Name: Brome mosaic virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 12302 / Sci species name: Brome mosaic virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes |
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-Macromolecule #1: Coat protein
Macromolecule | Name: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 180 / Enantiomer: LEVO |
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Source (natural) | Organism: Brome mosaic virus |
Molecular weight | Theoretical: 20.568693 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SNIMSTSGTG KMTRAQRRAA ARRNRRTAGV QPVIVEPIAA GQGKAIKAIA GYSISKWEAS SDAITAKATN AMSITLPHEL SSEKNKELK VGRVLLWLGL LPSVAGRIKA CVAEKQAQAE AAFQVALAVA DSSKEVVAAM YTDAFRGATL GDLLNLQIYL Y ASEAVPAK ...String: SNIMSTSGTG KMTRAQRRAA ARRNRRTAGV QPVIVEPIAA GQGKAIKAIA GYSISKWEAS SDAITAKATN AMSITLPHEL SSEKNKELK VGRVLLWLGL LPSVAGRIKA CVAEKQAQAE AAFQVALAVA DSSKEVVAAM YTDAFRGATL GDLLNLQIYL Y ASEAVPAK AVVVHLEVEH VRPTFDDFFT PVYK UniProtKB: Coat protein |
-Macromolecule #2: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 180 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 4.8 Details: 25 mM NaOAc pH 4.8, 5 mM MgCl2, 25 mM NaCl, 10 mM KCl |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 12569 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 3.0 µm / Calibrated defocus min: 0.9 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |