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- EMDB-3013: Electron cryo-microscopy of Cowpea Mosaic Virus containing RNA-1 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-3013
TitleElectron cryo-microscopy of Cowpea Mosaic Virus containing RNA-1 (CPMVb)
Map dataSingle particle reconstruction of wild type Cowpea mosaic virus containing RNA-1 (CPMVb)
Sample
  • Sample: Cowpea mosaic virus containing RNA-1
  • Virus: Cowpea mosaic virus
KeywordsCPMV / virus / comoviridae / picornavirales.
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 / GTP binding / host cell nucleus / 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: 3.44 Å
AuthorsHesketh EL / Meshcheriakova Y / Dent KC / Saxena P / Thompson R / Reddy V / Cockburn JJ / Lomonossoff GP / Ranson NA
CitationJournal: Nat Commun / Year: 2015
Title: Mechanisms of assembly and genome packaging in an RNA virus revealed by high-resolution cryo-EM.
Authors: Emma L Hesketh / Yulia Meshcheriakova / Kyle C Dent / Pooja Saxena / Rebecca F Thompson / Joseph J Cockburn / George P Lomonossoff / Neil A Ranson /
Abstract: Cowpea mosaic virus is a plant-infecting member of the Picornavirales and is of major interest in the development of biotechnology applications. Despite the availability of >100 crystal structures of ...Cowpea mosaic virus is a plant-infecting member of the Picornavirales and is of major interest in the development of biotechnology applications. Despite the availability of >100 crystal structures of Picornavirales capsids, relatively little is known about the mechanisms of capsid assembly and genome encapsidation. Here we have determined cryo-electron microscopy reconstructions for the wild-type virus and an empty virus-like particle, to 3.4 Å and 3.0 Å resolution, respectively, and built de novo atomic models of their capsids. These new structures reveal the C-terminal region of the small coat protein subunit, which is essential for virus assembly and which was missing from previously determined crystal structures, as well as residues that bind to the viral genome. These observations allow us to develop a new model for genome encapsidation and capsid assembly.
History
DepositionMay 13, 2015-
Header (metadata) releaseMay 27, 2015-
Map releaseDec 16, 2015-
UpdateAug 3, 2016-
Current statusAug 3, 2016Processing 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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  • Surface view with fitted model
  • Atomic models: PDB-5a32
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5a32
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3013-rad...

Downloads & links

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Map

FileDownload / File: emd_3013.map.gz / Format: CCP4 / Size: 210.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSingle particle reconstruction of wild type Cowpea mosaic virus containing RNA-1 (CPMVb)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 384 pix.
= 399.36 Å		1.04 Å/pix.
x 384 pix.
= 399.36 Å		1.04 Å/pix.
x 384 pix.
= 399.36 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: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.32711709 - 0.6045531
Average (Standard dev.)0.00177895 (±0.03853955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 399.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z399.360399.360399.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.3270.6050.002

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Supplemental data

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Supplemental map: emd 3013 additional 1.map

Fileemd_3013_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cowpea mosaic virus containing RNA-1

EntireName: Cowpea mosaic virus containing RNA-1
Components
  • Sample: Cowpea mosaic virus containing RNA-1
  • Virus: Cowpea mosaic virus

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Supramolecule #1000: Cowpea mosaic virus containing RNA-1

SupramoleculeName: Cowpea mosaic virus containing RNA-1 / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 3.71 MDa

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Supramolecule #1: Cowpea mosaic virus

SupramoleculeName: Cowpea mosaic virus / type: virus / ID: 1 / Name.synonym: CPMV / Details: Wild-type virus containing RNA-1 / NCBI-ID: 12264 / Sci species name: Cowpea mosaic virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: CPMV
Host (natural)Organism: Nicotiana benthamiana (plant) / synonym: PLANTAE(HIGHER PLANTS)
Molecular weightTheoretical: 3.71 MDa
Virus shellShell ID: 1 / Diameter: 280 Å / T number (triangulation number): 3

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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

Concentration5.8 mg/mL
GridDetails: 200 mesh quantifoil grids with 2 um holes, glow discharged
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 K / Max: 90 K
DateNov 1, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 1754 / Average electron dose: 45 e/Å2
Details: Images are averages of 16 images recorded on a Falcon II direct detector
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 134615 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 134615
Sample stageSpecimen holder: Liquid nitrogen cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsParticles were auto picked, classified using reference free 2D and furthered classified by several rounds of 3D classification prior to 3D auto refine, and movie processing.
CTF correctionDetails: CTFFIND3 per micrograph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: OTHER / Software - Name: RELION, 1.3 / Number images used: 4331
FSC plot (resolution estimation)

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