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- EMDB-1153: Kelp fly virus: a novel group of insect picorna-like viruses as d... -

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Basic information

Entry
Database: EMDB / ID: 1153
TitleKelp fly virus: a novel group of insect picorna-like viruses as defined by genome sequence analysis and a distinctive virion structure.
Map dataReconstruction of Kelp fly virus in which only a single vertex presents a turret
SampleKelp fly virus:
virus
SourceKelp fly virus (KFV)
Methodsingle particle reconstruction / cryo EM / 15 Å resolution
AuthorsHartley CJ / Greenwood DR / Gilbert RJC
CitationJournal: J. Virol. / Year: 2005
Title: Kelp fly virus: a novel group of insect picorna-like viruses as defined by genome sequence analysis and a distinctive virion structure.
Authors: C J Hartley / D R Greenwood / R J C Gilbert / A Masoumi / K H J Gordon / T N Hanzlik / E E Fry / D I Stuart / P D Scotti
DateDeposition: Aug 10, 2005 / Header (metadata) release: Aug 17, 2005 / Map release: Sep 2, 2005 / Last update: May 26, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 38.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 38.8
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_1153.map.gz (map file in CCP4 format, 10720 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
140 pix
4.38 Å/pix.
= 613.2 Å
140 pix
4.38 Å/pix.
= 613.2 Å
140 pix
4.38 Å/pix.
= 613.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.38 Å
Density
Contour Level:26.9, 38.8 (movie #1):
Minimum - Maximum-126.92 - 198.46
Average (Standard dev.)2.11162 (16.5256)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderZXY
Dimensions140140140
Origin-69-70-70
Limit706969
Spacing140140140
CellA=B=C: 613.2 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.384.384.38
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z613.200613.200613.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-69-70-70
NX/NY/NZ140140140
MAP C/R/S312
start NC/NR/NS-70-69-70
NC/NR/NS140140140
D min/max/mean-126.920198.4602.112

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Supplemental data

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Sample components

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Entire Kelp fly virus

EntireName: Kelp fly virus
Details: The sample displays evidence of a substoichiometric level of turret decoration.
Oligomeric State: One icosahedral virion / Number of components: 1
MassExperimental: 4.38 MDa
Measured by: Volumetrically from the reconstruction and by comparison with the known volume to mass ratio of other insect viruses

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Component #1: virus, Kelp fly virus

VirusName: Kelp fly virus / a.k.a: KFV / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
MassTheoretical: 4.38 MDa
SpeciesSpecies: Kelp fly virus (KFV)
Source (natural)Host Species: Chaetocoelopa sydneyensis / Host category: INVERTEBRATES
Shell #1Name of element: Capsid / Diameter: 330 Å
Shell #2Name of element: Capsid and turret / Diameter: 450 Å

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml / Buffer solution: 100 mM TRIS, pH 7.2 / pH: 7.2
Support film300 mesh copper grid, carbon lacey film
VitrificationCryogen name: ETHANE
Method: Blot until grid pulls away from Whatman number 1 paper before plunging

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG / Date: Jun 1, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 38000 X (nominal) / Astigmatism: objective lens astigmatism was corrected at / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 7000 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 100 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 27 / Scanner: OTHER / Sampling size: 4.38 microns / Bit depth: 8

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 3890 / Applied symmetry: C5 (5 fold cyclic)
3D reconstructionAlgorithm: Single particle / Software: SPIDER / CTF correction: By micrograph / Resolution: 15 Å / Resolution method: FSC 0.5 / Euler angles: SPIDER
Details: Final map was calculated from images that had previously been CTF-corrected. Map has a single turret on a unique vertex and has had 5fold symmetry applied after map calculation.

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