+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8592 | |||||||||
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Title | Subtomogram average of microtubules from PC12 cell | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Rattus (rat) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 64.0 Å | |||||||||
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_8592.map.gz | 399.5 KB | EMDB map data format | |
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Header (meta data) | emd-8592-v30.xml emd-8592.xml | 8.9 KB 8.9 KB | Display Display | EMDB header |
Images | emd_8592.png | 46.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8592 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8592 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8592.map.gz / Format: CCP4 / Size: 432.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 14.3 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 : Microtubule from PC12 cells
Entire | Name: Microtubule from PC12 cells |
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Components |
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-Supramolecule #1: Microtubule from PC12 cells
Supramolecule | Name: Microtubule from PC12 cells / type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Rattus (rat) / Tissue: adrenal medulla |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-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
Extraction | Number tomograms: 1 / Number images used: 677 / Method: Automated tomogram segmentation / Software - Name: EMAN (ver. 2.1) |
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Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 64.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN (ver. 2.2) / Number subtomograms used: 677 |