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- EMDB-1864: Cryo-EM reconstruction of native and expanded Turnip Crinkle virus -

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Database: EMDB / ID: 1864
TitleCryo-EM reconstruction of native and expanded Turnip Crinkle virus
KeywordsTurnip crinkle virus / genomic RNA structure / genome uncoating / ssRNA virus
SampleTurnip crinkle virus
SourceTurnip crinkle virus / virus
Map data3D cryo-EM reconstruction of the expanded form of Turnip Crinkle Virus
Methodsingle particle (icosahedral) reconstruction, at 17 Å resolution
AuthorsBakker SE / Robottom J / Pearson AR / Stockley PG / Ranson NA
CitationJ. Mol. Biol., 2012, 417, 65-78

primary. J. Mol. Biol., 2012, 417, 65-78 Yorodumi Papers
Isolation of an asymmetric RNA uncoating intermediate for a single-stranded RNA plant virus.
Saskia E Bakker / Robert J Ford / Amy M Barker / Janice Robottom / Keith Saunders / Arwen R Pearson / Neil A Ranson / Peter G Stockley

1. J. Mol. Biol., 1986, 191, 625-638 Yorodumi Papers
Structure and assembly of turnip crinkle virus. I. X-ray crystallographic structure analysis at 3.2 A resolution.
J M Hogle / A Maeda / S C Harrison

Validation ReportPDB-ID: 3zx9

SummaryFull reportAbout validation report
DateDeposition: Jan 25, 2011 / Header (metadata) release: Jul 9, 2012 / Map release: Jul 9, 2012 / Last update: Apr 30, 2014

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 3.2
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 3.2
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-3zx9
  • Surface level: 3.2
  • Imaged by UCSF CHIMERA
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-3zx9
  • Imaged by Jmol
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3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_1864.map.gz (map file in CCP4 format, 54001 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.89 Å/pix.
= 453.6 Å
240 pix
1.89 Å/pix.
= 453.6 Å
240 pix
1.89 Å/pix.
= 453.6 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.89 Å
Contour Level:3.2 (by author), 3.2 (movie #1):
Minimum - Maximum-1.86774302 - 4.17278814
Average (Standard dev.)0.16210388 (1.48636842)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 453.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.891.891.89
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z453.600453.600453.600
start NX/NY/NZ-160-160-159
MAP C/R/S123
start NC/NR/NS-120-120-120
D min/max/mean-1.8684.1730.162

Supplemental data

Sample components

Entire Turnip crinkle virus

EntireName: Turnip crinkle virus / Number of components: 1 / Oligomeric State: Icosahedral virus
MassTheoretical: 6.8 MDa

Component #1: virus, Turnip crinkle virus

VirusName: Turnip crinkle virus / a.k.a: Turnip crinkle virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
MassTheoretical: 6.8 MDa
SpeciesSpecies: Turnip crinkle virus / virus
Source (natural)Host Species: Brassica rapa subsp. rapa / plant / image: Brassica rapa
Shell #1Name of element: Expanded / Diameter: 380 Å / T number(triangulation number): 3

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 3 mg/ml / Buffer solution: 100 mM Tris pH 8.5, 5 mM EDTA / pH: 8.5
Support film400 mesh copper grid
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 77 K / Method: Blot 1.6 seconds before plunging
Details: Vitrification instrument: Double sided automated blotter and plunger

Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 52911 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3500 nm
Specimen HolderHolder: Gatan 626 / Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

Image acquisition

Image acquisitionNumber of digital images: 41 / Scanner: OTHER / Sampling size: 10 microns

Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 5121 / Number of class averages: 110 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Icosahedral / Software: SPIDER / CTF correction: Phase-flipping each particle / Resolution: 17 Å / Resolution method: FSC 0.5

Atomic model buiding

Output model

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