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- EMDB-6272: Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstro... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6272 | |||||||||
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Title | Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstroms resolution | |||||||||
![]() | Unsharpened reconstruction of rotavirus VP6 | |||||||||
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![]() | rotavirus / VP6 / cryo-EM / single particle | |||||||||
Function / homology | ![]() viral intermediate capsid / T=13 icosahedral viral capsid / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / structural molecule activity / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
![]() | Grant T / Grigorieff N | |||||||||
![]() | ![]() Title: Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6. Authors: Timothy Grant / Nikolaus Grigorieff / ![]() Abstract: Biological specimens suffer radiation damage when imaged in an electron microscope, ultimately limiting the attainable resolution. At a given resolution, an optimal exposure can be defined that ...Biological specimens suffer radiation damage when imaged in an electron microscope, ultimately limiting the attainable resolution. At a given resolution, an optimal exposure can be defined that maximizes the signal-to-noise ratio in the image. Using a 2.6 Å resolution single particle cryo-EM reconstruction of rotavirus VP6, determined from movies recorded with a total exposure of 100 electrons/Å(2), we obtained accurate measurements of optimal exposure values over a wide range of resolutions. At low and intermediate resolutions, our measured values are considerably higher than obtained previously for crystalline specimens, indicating that both images and movies should be collected with higher exposures than are generally used. We demonstrate a method of using our optimal exposure values to filter movie frames, yielding images with improved contrast that lead to higher resolution reconstructions. This 'high-exposure' technique should benefit cryo-EM work on all types of samples, especially those of relatively low-molecular mass. | |||||||||
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 | ![]() | 4.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.5 KB 10.5 KB | Display Display | ![]() |
Images | ![]() ![]() | 180.9 KB 145 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3j9sMC ![]() 6464C 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
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Annotation | Unsharpened reconstruction of rotavirus VP6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.023 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 : 13-fold average of VP6 trimer from full rotavirus reconstruction
Entire | Name: 13-fold average of VP6 trimer from full rotavirus reconstruction |
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Components |
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-Supramolecule #1000: 13-fold average of VP6 trimer from full rotavirus reconstruction
Supramolecule | Name: 13-fold average of VP6 trimer from full rotavirus reconstruction type: sample / ID: 1000 / Oligomeric state: Trimer / Number unique components: 1 |
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Molecular weight | Theoretical: 41 KDa |
-Macromolecule #1: Bovine rotavirus VP6
Macromolecule | Name: Bovine rotavirus VP6 / type: protein_or_peptide / ID: 1 / Name.synonym: Intermediate capsid protein VP6 / Number of copies: 3 / Oligomeric state: Trimer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 41 KDa |
Recombinant expression | Organism: ![]() |
Sequence | UniProtKB: Intermediate capsid protein VP6 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.5 mg/mL |
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Grid | Details: C-Flat 1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK II / Method: Blot for 4-6 seconds. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Legacy - Astigmatism: Corrected at 29,000 times magnification |
Date | Aug 13, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 531 / Average electron dose: 100 e/Å2 Details: 130-frame movies, 0.1 seconds per frame, 100e/A2 total dose. Super resolution. |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 48876 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Details | Additional 13-fold averaging was performed on top of the I symmetry. |
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CTF correction | Details: Each Particle |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: OTHER / Software - Name: TIGRIS, IMAGIC, FREALIGN Details: Final map is a 13-fold average of VP6 trimers from the asymmetric unit of the reconstruction of the whole capsid. Data at resolutions higher than 15A were not used for alignments. Number images used: 4000 |