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Yorodumi- EMDB-10451: ER microsome released with the code in (Martinez-Sanchez et al., ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10451 | |||||||||
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Title | ER microsome released with the code in (Martinez-Sanchez et al., Nature Methods) | |||||||||
Map data | ER microsome used in the code released in (Martinez-Sanchez et al., Nature Methods) | |||||||||
Sample |
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Biological species | Canis lupus familiaris (dog) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Martinez-Sanchez A / Lucic V / Pfeffer S / Forster F | |||||||||
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. #1: Journal: Nature Communications / Year: 2015 Title: Structure of the native Sec61 protein-conducting channel Authors: Pfeffer S / Forster F | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10451.map.gz | 4.9 MB | EMDB map data format | |
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Header (meta data) | emd-10451-v30.xml emd-10451.xml | 12.9 KB 12.9 KB | Display Display | EMDB header |
Images | emd_10451.png | 185.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10451 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10451 | HTTPS FTP |
-Validation report
Summary document | emd_10451_validation.pdf.gz | 217.4 KB | Display | EMDB validaton report |
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Full document | emd_10451_full_validation.pdf.gz | 216.5 KB | Display | |
Data in XML | emd_10451_validation.xml.gz | 4.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10451 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10451 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10451.map.gz / Format: CCP4 / Size: 5.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | ER microsome used in the code released in (Martinez-Sanchez et al., Nature Methods) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 10.48 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 : Representative tomogram of a canine pancreatic rough Endoplasmic ...
Entire | Name: Representative tomogram of a canine pancreatic rough Endoplasmic Reticulum vesicle. |
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Components |
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-Supramolecule #1: Representative tomogram of a canine pancreatic rough Endoplasmic ...
Supramolecule | Name: Representative tomogram of a canine pancreatic rough Endoplasmic Reticulum vesicle. type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Canis lupus familiaris (dog) / Tissue: pancreas |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Concentration | 2.00 mg/mL | ||||||||||||
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Buffer | pH: 7.6 Component:
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Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 70 % / Instrument: FEI VITROBOT MARK IV / Details: Blot 3 seconds before plunging.. | ||||||||||||
Sectioning | Other: NO SECTIONING | ||||||||||||
Fiducial marker | Manufacturer: Aurion, Wageningen, The Netherlands / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2 |
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: 4.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 42000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | Reconstruction of a single microsome after two binning steps (from 2.62A/pixel to 10.48A/pixel) |
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Final reconstruction | Software - Name: PyTom / Number images used: 61 |
CTF correction | Software - Name: PyTom |