|Entry||Database: EMDB / ID: 1316|
|Title||High-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus.|
|Sample||Tobacco Mosaic Virus|
|Source||Tobacco mosaic virus / virus / Virus|
|Map data||A 69 Angstrom section of the virus. The complete virus contains contains approximately 44 repeats of this 69 Angstrom section. The section contains 49 asymmetric units of the helical virus.Cube of 241 x 241 x 241 Angstrom|
|Method||helical reconstruction, at 4.4 Å resolution|
|Authors||Sachse C / Chen JZ / Coureux PD / Stroupe ME / Fandrich M / Grigorieff N|
|Citation||J. Mol. Biol., 2007, 371, 812-835|
|Validation Report||PDB-ID: 2om3|
SummaryFull reportAbout validation report
|Date||Deposition: Jan 22, 2007 / Header (metadata) release: Jan 22, 2007 / Map release: Jun 25, 2007 / Last update: Apr 13, 2016|
Downloads & links
|File||emd_1316.map.gz (map file in CCP4 format, 31251 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.163 Å|
CCP4 map header:
-Entire Tobacco Mosaic Virus
|Entire||Name: Tobacco Mosaic Virus / Number of components: 1|
|Mass||Theoretical: 37.5 MDa|
-Component #1: virus, Tobacco mosaic virus
|Helical parameters||Axial symmetry: C1 (asymmetric) / Hand: RIGHT HANDED|
|Sample solution||Specimen conc.: 2.5 mg/ml / Buffer solution: Phosphate (5mM EDTA) / pH: 7.4|
|Support film||Quantifoil grid|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277.15 K / Method: Blot for 2 seconds before plunging / Details: Vitrification instrument: self-built model|
-Electron microscopy imaging
Model: Tecnai F30 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F30 / Date: Nov 22, 2005|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 59000 X (nominal), 60190 X (calibrated)|
Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 4500 nm
|Specimen Holder||Holder: Side entry liquid nitrogen-cooled cryo specimen holder|
Model: GATAN LIQUID NITROGEN / Temperature: 93 K ( 93 - 93 K)
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 6 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8|
|Processing||Method: helical reconstruction|
|3D reconstruction||Algorithm: SIRT - iterative algebraic reconstruction methods|
CTF correction: CTFFIND and CTFTILT phase-correction and amplitude-weighting of each paritcle after Grigorieff 1998
Resolution: 4.4 Å / Resolution method: 5
Details: Final map was calculated from the central 241x241x241 cube.
-Atomic model buiding
|Modeling #1||Software: XPLOR / Refinement protocol: flexible|
Target criteria: minimization of of least-square difference between observed and calculated densities
Refinement space: REAL
Details: Protocol: Torsion angle dynamics. 2TMV pdb code structure was adjusted to fit the density for residues 88-109 and refined
Input PDB model: 2OM3
Chain ID: A, R
Overall bvalue: 90
-Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
- Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
- Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.
External links: The 2017 Nobel Prize in Chemistry - Press Release
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