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Yorodumi- EMDB-10439: Example of tomogram used for in situ template-free membrane bound... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10439 | |||||||||
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Title | Example of tomogram used for in situ template-free membrane bound complexes determination | |||||||||
Map data | Example of tomogram used for in situ template-free membrane bound complexes determination | |||||||||
Sample |
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Biological species | Mus musculus (house mouse) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Martinez-Sanchez A / Lucic V / Chakraborty S | |||||||||
Funding support | Spain, 1 items
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Citation | Journal: Nat Methods / Year: 2020 Title: Template-free detection and classification of membrane-bound complexes in cryo-electron tomograms. Authors: Antonio Martinez-Sanchez / Zdravko Kochovski / Ulrike Laugks / Johannes Meyer Zum Alten Borgloh / Saikat Chakraborty / Stefan Pfeffer / Wolfgang Baumeister / Vladan Lučić / Abstract: With faithful sample preservation and direct imaging of fully hydrated biological material, cryo-electron tomography provides an accurate representation of molecular architecture of cells. However, ...With faithful sample preservation and direct imaging of fully hydrated biological material, cryo-electron tomography provides an accurate representation of molecular architecture of cells. However, detection and precise localization of macromolecular complexes within cellular environments is aggravated by the presence of many molecular species and molecular crowding. We developed a template-free image processing procedure for accurate tracing of complex networks of densities in cryo-electron tomograms, a comprehensive and automated detection of heterogeneous membrane-bound complexes and an unsupervised classification (PySeg). Applications to intact cells and isolated endoplasmic reticulum (ER) allowed us to detect and classify small protein complexes. This classification provided sufficiently homogeneous particle sets and initial references to allow subsequent de novo subtomogram averaging. Spatial distribution analysis showed that ER complexes have different localization patterns forming nanodomains. Therefore, this procedure allows a comprehensive detection and structural analysis of complexes in situ. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10439.map.gz | 1.5 GB | EMDB map data format | |
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Header (meta data) | emd-10439-v30.xml emd-10439.xml | 10.4 KB 10.4 KB | Display Display | EMDB header |
Images | emd_10439.png | 289.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10439 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10439 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10439.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Example of tomogram used for in situ template-free membrane bound complexes determination | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 13.68 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 : Intact P19 cells
Entire | Name: Intact P19 cells |
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Components |
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-Supramolecule #1: Intact P19 cells
Supramolecule | Name: Intact P19 cells / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Mus musculus (house mouse) / Tissue: teratocarcinoma |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 90 % / Chamber temperature: 310.15 K / Instrument: FEI VITROBOT MARK IV |
Sectioning | Other: NO SECTIONING |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 0.25 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 42000 |
Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Slit width: 20 eV |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: RELION (ver. 2.1) Details: Original reconstructed pixel size is 3.42 Angstroms, however due to size restriction a 4-times binned version with 13.68 Angstroms per pixel is provided here Number images used: 60 |
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