+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8594 | |||||||||
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Title | Automated tomogram annotation of PC12 cell | |||||||||
Map data | Automated tomogram annotation of PC12 cell | |||||||||
Sample |
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Biological species | Rattus (rat) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Chen M / Dai W / Schmid MF / Chiu W / Ludtke SJ | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Methods / Year: 2017 Title: Convolutional neural networks for automated annotation of cellular cryo-electron tomograms. Authors: Muyuan Chen / Wei Dai / Stella Y Sun / Darius Jonasch / Cynthia Y He / Michael F Schmid / Wah Chiu / Steven J Ludtke / Abstract: Cellular electron cryotomography offers researchers the ability to observe macromolecules frozen in action in situ, but a primary challenge with this technique is identifying molecular components ...Cellular electron cryotomography offers researchers the ability to observe macromolecules frozen in action in situ, but a primary challenge with this technique is identifying molecular components within the crowded cellular environment. We introduce a method that uses neural networks to dramatically reduce the time and human effort required for subcellular annotation and feature extraction. Subsequent subtomogram classification and averaging yield in situ structures of molecular components of interest. The method is available in the EMAN2.2 software package. | |||||||||
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_8594.map.gz | 206.9 MB | EMDB map data format | |
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Header (meta data) | emd-8594-v30.xml emd-8594.xml | 16.1 KB 16.1 KB | Display Display | EMDB header |
Images | emd_8594.png | 346.1 KB | ||
Others | emd_8594_additional_1.map.gz emd_8594_additional_2.map.gz emd_8594_additional_3.map.gz emd_8594_additional_4.map.gz | 124.8 MB 137.4 MB 98.5 MB 113.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8594 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8594 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8594.map.gz / Format: CCP4 / Size: 223.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Automated tomogram annotation of PC12 cell | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 28.6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Automatic annotation of double layer membrane in PC12 cell
File | emd_8594_additional_1.map | ||||||||||||
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Annotation | Automatic annotation of double layer membrane in PC12 cell | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Automatic annotation of microtubules in PC12 cell
File | emd_8594_additional_2.map | ||||||||||||
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Annotation | Automatic annotation of microtubules in PC12 cell | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Automatic annotation of ribosomes in PC12 cell
File | emd_8594_additional_3.map | ||||||||||||
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Annotation | Automatic annotation of ribosomes in PC12 cell | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Automatic annotation of single layer membrane in PC12 cell
File | emd_8594_additional_4.map | ||||||||||||
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Annotation | Automatic annotation of single layer membrane in PC12 cell | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : PC12 cell
Entire | Name: PC12 cell |
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Components |
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-Supramolecule #1: PC12 cell
Supramolecule | Name: PC12 cell / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Rattus (rat) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: EMS / Diameter: 14 nm |
-Electron microscopy
Microscope | JEOL 2100 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 2.0 e/Å2 |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Number images used: 30 |
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