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- EMDB-3952: CPMV eVLP -

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Basic information

Entry
Database: EMDB / ID: EMD-3952
TitleCPMV eVLP
Map dataCowpea mosaic virus empty virus like particle
Sample
  • Virus: Cowpea mosaic virus
Biological speciesCowpea mosaic virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
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 non- ...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.
History
DepositionOct 26, 2017-
Header (metadata) releaseNov 15, 2017-
Map releaseDec 27, 2017-
UpdateDec 27, 2017-
Current statusDec 27, 2017Processing site: PDBe / Status: Released

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Structure visualization

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

emd_3952.png

Downloads & links

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Map

FileDownload / File: emd_3952.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCowpea mosaic virus empty virus like particle
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.21496366 - 0.36677027
Average (Standard dev.)0.00047987353 (±0.02091691)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 447.34198 Å
α=β=γ: 90.0 °

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
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
Components
  • Virus: Cowpea mosaic virus

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Supramolecule #1: Cowpea mosaic virus

SupramoleculeName: Cowpea mosaic virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 12264 / Sci species name: Cowpea mosaic virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host systemOrganism: NICOTIANA BENTHAMIANA (plant)

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 67.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: EMDB MAP
EMDB ID:

3014

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 280000
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
FSC plot (resolution estimation)

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