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- EMDB-13344: Cryo-EM structure of BMV-derived VLP expressed in E. coli and ass... -

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Basic information

Entry
Database: EMDB / ID: EMD-13344
TitleCryo-EM structure of BMV-derived VLP expressed in E. coli and assembled in the presence of tRNA (tVLP)
Map data
Sample
  • Virus: Brome mosaic virus
    • Protein or peptide: Coat protein
  • Ligand: water
KeywordsBMV / brome mosaic virus / capsid proteins / VIRUS LIKE PARTICLE
Function / homologyBromovirus coat protein / Bromovirus coat protein / viral capsid / structural molecule activity / Coat protein
Function and homology information
Biological speciesBrome mosaic virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsRuszkowski M / Strugala A
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionAug 9, 2021-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7pe1
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7pe1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13344.png

Downloads & links

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Map

FileDownload / File: emd_13344.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 512 pix.
= 440.32 Å		0.86 Å/pix.
x 512 pix.
= 440.32 Å		0.86 Å/pix.
x 512 pix.
= 440.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.02727989 - 0.057529032
Average (Standard dev.)0.00025860703 (±0.003915549)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 440.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z440.320440.320440.320
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0270.0580.000

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Supplemental data

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Sample components

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Entire : Brome mosaic virus

EntireName: Brome mosaic virus
Components
  • Virus: Brome mosaic virus
    • Protein or peptide: Coat protein
  • Ligand: water

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Supramolecule #1: Brome mosaic virus

SupramoleculeName: 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: No

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Macromolecule #1: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 180 / Enantiomer: LEVO
Source (natural)Organism: Brome mosaic virus
Molecular weightTheoretical: 20.568693 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 180 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 4.8
Details: 25 mM NaOAc pH 4.8, 5 mM MgCl2, 25 mM NaCl, 10 mM KCl
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 17955 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated 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

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Image processing

Particle selectionNumber selected: 1419349
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6voc

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 24812
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6voc


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7pe1:
Cryo-EM structure of BMV-derived VLP expressed in E. coli and assembled in the presence of tRNA (tVLP)

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