|Entry||Database: EMDB / ID: EMD-1863|
|Title||Cryo-EM reconstruction of native and expanded Turnip Crinkle virus|
|Sample||Turnip crinkle virus:|
|Keywords||turnip crinkle virus / genomic RNA structure / genome uncoating / ssRNA virus|
|Function / homology||Plant viruses icosahedral capsid proteins 'S' region signature. / Viral coat protein (S domain) / Icosahedral viral capsid protein, S domain / T=3 icosahedral viral capsid / Viral coat protein subunit / structural molecule activity / viral process / RNA binding / Capsid protein|
Function and homology information
|Biological species||Turnip crinkle virus|
|Method||single particle reconstruction / cryo EM / Resolution: 11.5 Å|
|Authors||Bakker SE / Robottom J / Pearson AR / Stockley PG / Ranson NA|
|Citation||Journal: J Mol Biol / Year: 1986|
Title: Structure and assembly of turnip crinkle virus. I. X-ray crystallographic structure analysis at 3.2 A resolution.
Abstract: The structure of turnip crinkle virus has been determined at 3.2 A resolution, using the electron density of tomato bushy stunt virus as a starting point for phase refinement by non-crystallographic ...The structure of turnip crinkle virus has been determined at 3.2 A resolution, using the electron density of tomato bushy stunt virus as a starting point for phase refinement by non-crystallographic symmetry. The structures are very closely related, especially in the subunit arm and S domain, where only small insertions and deletions and small co-ordinate shifts relate one chain to another. The P domains, although quite similar in fold, are oriented somewhat differently with respect to the S domains. Understanding of the structure of turnip crinkle virus has been important for analyzing its assembly, as described in an accompanying paper.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_1863.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.323 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Turnip crinkle virus
|Entire||Name: Turnip crinkle virus / Number of components: 1 / Oligomeric State: Icosahedral virus|
|Mass||Theoretical: 6.8 MDa|
-Component #1: virus, Turnip crinkle virus
|Virus||Name: Turnip crinkle virus / a.k.a: Turnip crinkle virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN|
|Mass||Theoretical: 6.8 MDa|
|Species||Species: Turnip crinkle virus|
|Source (natural)||Host Species: Brassica rapa subsp. rapa (turnip)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 2 mg/mL|
Buffer solution: 10 mM sodium phosphate pH 7.4, 10 mM magnesium sulphate
|Support film||400 mesh copper grid|
|Vitrification||Instrument: 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
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 50000 X (nominal), 52911 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3500 nm|
|Specimen Holder||Holder: Gatan 626 / Model: GATAN LIQUID NITROGEN|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 70 / Scanner: ZEISS SCAI / Sampling size: 7 µm|
|Processing||Method: single particle reconstruction / Number of projections: 18681 / Number of class averages: 331 / Applied symmetry: I (正20面体型対称)|
|3D reconstruction||Algorithm: Icosahedral / Software: SPIDER / CTF correction: Phase-flipping each particle / Resolution: 11.5 Å / Resolution method: FSC 0.5|
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