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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: 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
SampleCowpea mosaic virus
SourceCowpea mosaic virus / virus
Map dataCowpea mosaic virus (CPMV) cleaved eVLP structure
Methodsingle particle (icosahedral) reconstruction, at 4.4 A resolution
AuthorsHesketh EL / Thompson RF / Ranson NA
CitationSci Rep, 2017, 7, 539-539

Sci Rep, 2017, 7, 539-539 StrPapers
The structures of a naturally empty cowpea mosaic virus particle and its genome-containing counterpart by cryo-electron microscopy.
Emma L Hesketh / Yulia Meshcheriakova / Rebecca F Thompson / George P Lomonossoff / Neil A Ranson

DateDeposition: Feb 20, 2017 / Header (metadata) release: Apr 5, 2017 / Map release: Apr 12, 2017 / Last update: Feb 20, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.07
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_8609.map.gz (map file in CCP4 format, 442369 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
480 pix
1.04 A/pix
= 499.2 A
480 pix
1.04 A/pix
= 499.2 A
480 pix
1.04 A/pix
= 499.2 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.04 A
Density
Contour Level:0.07 (by author), 0.07 (movie #1):
Minimum - Maximum-0.0803581 - 0.20112681
Average (Standard dev.)0.0021032945 (0.012859347)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions480480480
Origin000
Limit479479479
Spacing480480480
CellA=B=C: 499.19998 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
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
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
Number of components: 1
MassTheoretical: 3.87 MDa

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Component #1: virus, Cowpea mosaic virus

VirusName: Cowpea mosaic virus / Class: VIRUS-LIKE PARTICLE
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
Empty: Yes / Enveloped: No / Isolate: STRAIN
MassTheoretical: 3.87 MDa
SpeciesSpecies: Cowpea mosaic virus / virus
Source (engineered)Expression System: Nicotiana benthamiana / plant / image: Nicotiana tabacum
Source (natural)Host Species: Vigna unguiculata / plant

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 4.2 mg/ml / Buffer solution: Phosphate buffer pH 7.0 / pH: 7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 94 K / Humidity: 100 %

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 134615 X (nominal), 134615 X (calibrated) / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 90 - 90 K)
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1135

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 1537
3D reconstructionSoftware: relion / Resolution: 4.4 A / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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