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- EMDB-1864: Cryo-EM reconstruction of native and expanded Turnip Crinkle virus -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1864 | |||||||||
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Title | Cryo-EM reconstruction of native and expanded Turnip Crinkle virus | |||||||||
![]() | 3D cryo-EM reconstruction of the expanded form of Turnip Crinkle Virus | |||||||||
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![]() | Turnip crinkle virus / genomic RNA structure / genome uncoating / ssRNA virus | |||||||||
Function / homology | Plant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / T=3 icosahedral viral capsid / Viral coat protein subunit / virus-mediated perturbation of host defense response / structural molecule activity / RNA binding / Capsid protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 17.0 Å | |||||||||
![]() | Bakker SE / Robottom J / Pearson AR / Stockley PG / Ranson NA | |||||||||
![]() | ![]() 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. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 48 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10 KB 10 KB | Display Display | ![]() |
Images | ![]() | 151.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 224.8 KB | Display | ![]() |
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Full document | ![]() | 224 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zx9MC ![]() 1863C ![]() 3zx8C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D cryo-EM reconstruction of the expanded form of Turnip Crinkle Virus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.89 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Turnip crinkle virus
Entire | Name: ![]() |
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Components |
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-Supramolecule #1000: Turnip crinkle virus
Supramolecule | Name: Turnip crinkle virus / type: sample / ID: 1000 / Oligomeric state: Icosahedral virus / Number unique components: 1 |
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Molecular weight | Theoretical: 6.8 MDa |
-Supramolecule #1: Turnip crinkle virus
Supramolecule | Name: Turnip crinkle virus / type: virus / ID: 1 / Name.synonym: Turnip crinkle virus / NCBI-ID: 11988 / Sci species name: Turnip crinkle virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Turnip crinkle virus |
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Host (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 6.8 MDa |
Virus shell | Shell ID: 1 / Name: Expanded / Diameter: 380 Å / T number (triangulation number): 3 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 8.5 / Details: 100 mM Tris pH 8.5, 5 mM EDTA |
Grid | Details: 400 mesh copper grid |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 77 K / Instrument: HOMEMADE PLUNGER Details: Vitrification instrument: Double sided automated blotter and plunger Method: Blot 1.6 seconds before plunging |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 10 µm / Number real images: 41 / Average electron dose: 15 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 52911 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: Phase-flipping each particle |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 5121 |
Final two d classification | Number classes: 110 |