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- EMDB-2835: Cryo-EM structure of TMV reconstructed from data ranging from 2.0... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2835 | |||||||||
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Title | Cryo-EM structure of TMV reconstructed from data ranging from 2.0-6.1 e-/A^2 accumulated dose | |||||||||
![]() | Cryo-EM structure of TMV reconstructed from data ranging from 2.0-6.1 e-/A^2 accumulated dose | |||||||||
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![]() | tobacco mosaic virus / direct electron detectors / single particle helical reconstruction / radiation damage | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Fromm SA / Bharat TAM / Jakobi AJ / Hagen WJH / Sachse C | |||||||||
![]() | ![]() Title: Seeing tobacco mosaic virus through direct electron detectors. Authors: Simon A Fromm / Tanmay A M Bharat / Arjen J Jakobi / Wim J H Hagen / Carsten Sachse / ![]() ![]() Abstract: With the introduction of direct electron detectors (DED) to the field of electron cryo-microscopy, a wave of atomic-resolution structures has become available. As the new detectors still require ...With the introduction of direct electron detectors (DED) to the field of electron cryo-microscopy, a wave of atomic-resolution structures has become available. As the new detectors still require comparative characterization, we have used tobacco mosaic virus (TMV) as a test specimen to study the quality of 3D image reconstructions from data recorded on the two direct electron detector cameras, K2 Summit and Falcon II. Using DED movie frames, we explored related image-processing aspects and compared the performance of micrograph-based and segment-based motion correction approaches. In addition, we investigated the effect of dose deposition on the atomic-resolution structure of TMV and show that radiation damage affects negative carboxyl chains first in a side-chain specific manner. Finally, using 450,000 asymmetric units and limiting the effects of radiation damage, we determined a high-resolution cryo-EM map at 3.35Å resolution. Here, we provide a comparative case study of highly ordered TMV recorded on different direct electron detectors to establish recording and processing conditions that enable structure determination up to 3.2Å in resolution using cryo-EM. | |||||||||
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 | ![]() | 23.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.6 KB 10.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.5 KB | Display | ![]() |
Images | ![]() | 280.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 348.7 KB | Display | ![]() |
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Full document | ![]() | 347.8 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2833C ![]() 2834C ![]() 2836C ![]() 2837C ![]() 2838C ![]() 2839C ![]() 2840C ![]() 2841C ![]() 2842C ![]() 4udvC C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 47.7 Data #1: Tobacco Mosaic Virus micrographs [micrographs - multiframe]) |
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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 | Cryo-EM structure of TMV reconstructed from data ranging from 2.0-6.1 e-/A^2 accumulated dose | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.062 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 : Tobacco Mosaic Virus
Entire | Name: ![]() ![]() |
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Components |
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-Supramolecule #1000: Tobacco Mosaic Virus
Supramolecule | Name: Tobacco Mosaic Virus / type: sample / ID: 1000 / Details: The sample was purified from infected leaves. / Oligomeric state: helical / Number unique components: 1 |
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Molecular weight | Theoretical: 39.5 MDa |
-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 / Sci species strain: vulgare / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: TMV |
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Host (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 39.5 MDa |
Virus shell | Shell ID: 1 / Name: CP / Diameter: 180 Å |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Concentration | 11.0 mg/mL |
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Buffer | pH: 7 / Details: 50 mM NaPO4 |
Grid | Details: Quantifoil 2/2 Cu 200 mesh grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 95 K / Instrument: FEI VITROBOT MARK III Method: Blot for 8 seconds with an offset of -2 mm ~30-45 seconds after sample application |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Legacy - Astigmatism: CTFTILT |
Details | Nanoprobe mode, dose rate ~41 e-/px/s on the camera level, fully automated acquisition using FEI EPU software |
Date | Oct 16, 2013 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 109 / Average electron dose: 30.7 e/Å2 Details: each micrograph was recorded as a movie of 7 frames excluding the roll-in frame corresponding to 2 e-/A^2 accumulated dose which was discarded |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 131827 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |