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Yorodumi- EMDB-1730: 4.6 Angstrom Cryo-EM reconstruction of Tobacco Mosaic Virus from ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1730 | |||||||||
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Title | 4.6 Angstrom Cryo-EM reconstruction of Tobacco Mosaic Virus from images recorded at 300 KeV on a 4kx4k CCD camera | |||||||||
Map data | B-factor scaled fully CTF corrected density map of TMV | |||||||||
Sample |
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Keywords | Cryo-EM / single particle processing / TMV / CCD data / 300 KeV electrons | |||||||||
Function / homology | Tobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / helical viral capsid / structural molecule activity / Capsid protein Function and homology information | |||||||||
Biological species | Tobacco mosaic virus | |||||||||
Method | helical reconstruction / cryo EM / negative staining / Resolution: 4.6 Å | |||||||||
Authors | Clare DK / Orlova EV | |||||||||
Citation | Journal: J Struct Biol / Year: 2010 Title: 4.6A Cryo-EM reconstruction of tobacco mosaic virus from images recorded at 300 keV on a 4k x 4k CCD camera. Authors: Daniel K Clare / Elena V Orlova / Abstract: Tobacco mosaic virus (TMV) is a plant virus with a highly ordered organisation and has been described in three different structural states: As stacked disks without RNA (X-ray crystallography), as a ...Tobacco mosaic virus (TMV) is a plant virus with a highly ordered organisation and has been described in three different structural states: As stacked disks without RNA (X-ray crystallography), as a helical form with RNA (X-ray fibre diffraction) and as a second distinct helical form with RNA (cryo-EM). Here we present a structural analysis of TMV as a test object to assess the quality of cryo-EM images recorded at 300 keV on a CCD camera. The 4.6A TMV structure obtained is consistent with the previous cryo-EM structure and confirms that there is a second helical form of TMV. The structure here also shows that with a similar number of TMV segments an equivalent resolution can be achieved with a 4k CCD camera at 300 keV. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1730.map.gz | 16.5 MB | EMDB map data format | |
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Header (meta data) | emd-1730-v30.xml emd-1730.xml | 12.2 KB 12.2 KB | Display Display | EMDB header |
Images | 1730.png | 492.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1730 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1730 | HTTPS FTP |
-Validation report
Summary document | emd_1730_validation.pdf.gz | 337 KB | Display | EMDB validaton report |
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Full document | emd_1730_full_validation.pdf.gz | 336.2 KB | Display | |
Data in XML | emd_1730_validation.xml.gz | 6.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1730 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1730 | HTTPS FTP |
-Related structure data
Related structure data | 2xeaMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1730.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | B-factor scaled fully CTF corrected density map of TMV | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Tobacco Mosaic Virus
Entire | Name: Tobacco Mosaic Virus |
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Components |
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-Supramolecule #1000: Tobacco Mosaic Virus
Supramolecule | Name: Tobacco Mosaic Virus / type: sample / ID: 1000 / Details: Monodisperse Oligomeric state: Homo-oligomer of TMV coat protein and ssRNA Number unique components: 2 |
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Molecular weight | Experimental: 175 KDa / Theoretical: 175 KDa |
-Supramolecule #1: Tobacco mosaic virus
Supramolecule | Name: Tobacco mosaic virus / type: virus / ID: 1 / Name.synonym: TMV / NCBI-ID: 12242 / Sci species name: Tobacco mosaic virus / Database: NCBI / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No / Syn species name: TMV |
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Host (natural) | Organism: Nicotiana (plant) / synonym: PLANTAE(HIGHER PLANTS) |
Molecular weight | Experimental: 175 KDa / Theoretical: 175 KDa |
Virus shell | Shell ID: 1 / Name: CP / Diameter: 180 Å |
-Macromolecule #1: ssRNA
Macromolecule | Name: ssRNA / type: rna / ID: 1 / Name.synonym: RNA / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No |
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Source (natural) | Organism: Tobacco mosaic virus / synonym: TMV |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 7.4 / Details: 50 mM Tris-HCl, 50 mM KCl, 10 mM MgCl2 |
Staining | Type: NEGATIVE Details: 3.5ul of TMV was added to R2/2 C-flat grid, blotted, then plunge frozen in liquid ethane |
Grid | Details: 400 mesh R2/2 c-flat grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 60 % / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Home made plunger Method: Grids were blotted for around 2 seconds and then rapidly plunged into liquid ethane |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Average: 78 K |
Alignment procedure | Legacy - Astigmatism: Corrected at 115,000 times |
Date | Feb 1, 2009 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 104 / Average electron dose: 25 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 121000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 90000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN HELIUM |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | The particle were selected using the helical option in boxer |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 1.408 Å Applied symmetry - Helical parameters - Δ&Phi: 22.04 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, IMAGIC / Details: BPRP was used for reconstruction |
CTF correction | Details: Each particle was fully CTF corrected |
Final angle assignment | Details: 80-100 in theta and 0-22.04 in phi in 0.5 steps |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera and Coot |
Details | Protocol: Rigid body, real space. The PDB was initially fitted using chimera, the coordinates were then refined using Coot |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient |
Output model | PDB-2xea: |