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- EMDB-8609: Cleaved Cowpea Mosaic Virus (CPMV) eVLP structure refined from a ... -

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Basic information

Entry
Database: EMDB / ID: EMD-8609
TitleCleaved Cowpea Mosaic Virus (CPMV) eVLP structure refined from a small subset of data from the cryo-EM reconstruction of uncleaved eVLP reported previously
Map dataCowpea mosaic virus (CPMV) cleaved eVLP structure
Sample
  • Virus: Cowpea mosaic virus
Function / homology
Function and homology information


transport of virus in host, cell to cell / host cell plasmodesma / T=3 icosahedral viral capsid / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response / host cell nucleus / GTP binding / structural molecule activity / DNA binding / RNA binding
Similarity search - Function
Large coat protein / RNA2 polyprotein / Large coat protein / Small coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesCowpea mosaic virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsHesketh EL / Thompson RF / Ranson NA
CitationJournal: Sci Rep / Year: 2017
Title: The structures of a naturally empty cowpea mosaic virus particle and its genome-containing counterpart by cryo-electron microscopy.
Authors: Emma L Hesketh / Yulia Meshcheriakova / Rebecca F Thompson / George P Lomonossoff / Neil A Ranson /
Abstract: Cowpea mosaic virus (CPMV) is a picorna-like plant virus. As well as an intrinsic interest in CPMV as a plant pathogen, CPMV is of major interest in biotechnology applications such as nanotechnology. ...Cowpea mosaic virus (CPMV) is a picorna-like plant virus. As well as an intrinsic interest in CPMV as a plant pathogen, CPMV is of major interest in biotechnology applications such as nanotechnology. Here, we report high resolution cryo electron microscopy (cryo-EM) maps of wild type CPMV containing RNA-2, and of naturally-formed empty CPMV capsids. The resolution of these structures is sufficient to visualise large amino acids. We have refined an atomic model for each map and identified an essential amino acid involved in genome encapsidation. This work has furthered our knowledge of Picornavirales genome encapsidation and will assist further work in the development of CPMV as a biotechnological tool.
History
DepositionFeb 20, 2017-
Header (metadata) releaseApr 5, 2017-
Map releaseApr 12, 2017-
UpdateJan 31, 2018-
Current statusJan 31, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8609.png

Downloads & links

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Map

FileDownload / File: emd_8609.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCowpea mosaic virus (CPMV) cleaved eVLP structure
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 480 pix.
= 499.2 Å		1.04 Å/pix.
x 480 pix.
= 499.2 Å		1.04 Å/pix.
x 480 pix.
= 499.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.0803581 - 0.20112681
Average (Standard dev.)0.0021032945 (±0.012859347)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 499.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z499.200499.200499.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0800.2010.002

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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
Details: Empty virus like particles (eVLPs) produced by expressing a coat precursor protein VP60 which expressed both large and small proteins and the 24K protease in N. benthamiana
NCBI-ID: 12264 / Sci species name: Cowpea mosaic virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Vigna unguiculata (cowpea)
Host systemOrganism: Nicotiana benthamiana (plant)
Molecular weightTheoretical: 3.87 MDa
Virus shellShell ID: 1 / Diameter: 280.0 Å

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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

Concentration4.2 mg/mL
BufferpH: 7 / Details: Phosphate buffer pH 7.0
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 1.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 94 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 90.0 K / Max: 90.0 K
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1135 / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 134615 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 134615
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 62514
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: OTHER / Details: Sphere with a radius of 155 A
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 1537
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.3)
FSC plot (resolution estimation)

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