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- EMDB-3952: CPMV eVLP -

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Basic information

Entry
Database: EMDB / ID: 3952
TitleCPMV eVLP
Map dataCowpea mosaic virus empty virus like particle
SampleCowpea mosaic virus:
virus
SourceCowpea mosaic virus
Methodsingle particle reconstruction / cryo EM / 2.7 Å resolution
AuthorsMeshcheriakova Y / Durrant A / Hesketh EL / Ranson NA / Lomonossoff GP
CitationJournal: Biochem. Soc. Trans. / Year: 2017
Title: Combining high-resolution cryo-electron microscopy and mutagenesis to develop cowpea mosaic virus for bionanotechnology.
Authors: Yulia Meshcheriakova / Alex Durrant / Emma L Hesketh / Neil A Ranson / George P Lomonossoff
Abstract: Particles of cowpea mosaic virus (CPMV) have enjoyed considerable success as nanoparticles. The development of a system for producing empty virus-like particles (eVLPs) of the virus, which are ...Particles of cowpea mosaic virus (CPMV) have enjoyed considerable success as nanoparticles. The development of a system for producing empty virus-like particles (eVLPs) of the virus, which are non-infectious and have the potential to be loaded with heterologous material, has increased the number of possible applications for CPMV-based particles. However, for this potential to be realised, it was essential to demonstrate that eVLPs were accurate surrogates for natural virus particles, and this information was provided by high-resolution cryo-EM studies of eVLPs. This demonstration has enabled the approaches developed for the production of modified particles developed with natural CPMV particles to be applied to eVLPs. Furthermore, a combination of cryo-EM and mutagenic studies allowed the development of particles which are permeable but which could still assemble efficiently. These particles were shown to be loadable with cobalt, indicating that they can, indeed, be used as nano-containers.
DateDeposition: Oct 26, 2017 / Header (metadata) release: Nov 15, 2017 / Map release: Dec 27, 2017 / Last update: Dec 27, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3952.map.gz (map file in CCP4 format, 296353 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
420 pix
1.07 Å/pix.
= 447.342 Å
420 pix
1.07 Å/pix.
= 447.342 Å
420 pix
1.07 Å/pix.
= 447.342 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0651 Å
Density
Contour Level:0.09 (by author), 0.09 (movie #1):
Minimum - Maximum-0.21496366 - 0.36677027
Average (Standard dev.)0.00047987353 (0.02091691)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions420420420
Origin000
Limit419419419
Spacing420420420
CellA=B=C: 447.34198 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.06511.06511.0651
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z447.342447.342447.342
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.2150.3670.000

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Supplemental data

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Sample components

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Entire Cowpea mosaic virus

EntireName: Cowpea mosaic virus / Number of components: 1

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Component #1: virus, Cowpea mosaic virus

VirusName: Cowpea mosaic virus / Class: VIRUS-LIKE PARTICLE / Empty: Yes / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Cowpea mosaic virus
Source (engineered)Expression System: NICOTIANA BENTHAMIANA (plant)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 67.5 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 280000
3D reconstructionSoftware: RELION / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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