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Yorodumi- EMDB-15152: Cryo-electron tomogram of secreted particles from Apilactobacillu... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15152 | |||||||||
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Title | Cryo-electron tomogram of secreted particles from Apilactobacillus kunkeei (TS_03) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Membrane vesicles / extracellular protein complexes / UNKNOWN FUNCTION | |||||||||
Biological species | Apilactobacillus kunkeei (bacteria) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Seeger C / Andersson SGE | |||||||||
Funding support | Sweden, 1 items
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Citation | Journal: To Be Published Title: Cryo-eletron tomogram of secreted particles from Apilactobacillus kunkeei (TS_01) Authors: Seeger C / Andersson SGE | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15152.map.gz | 12.3 MB | EMDB map data format | |
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Header (meta data) | emd-15152-v30.xml emd-15152.xml | 8.2 KB 8.2 KB | Display Display | EMDB header |
Images | emd_15152.png | 252.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15152 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15152 | HTTPS FTP |
-Validation report
Summary document | emd_15152_validation.pdf.gz | 544.3 KB | Display | EMDB validaton report |
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Full document | emd_15152_full_validation.pdf.gz | 543.8 KB | Display | |
Data in XML | emd_15152_validation.xml.gz | 2 KB | Display | |
Data in CIF | emd_15152_validation.cif.gz | 2.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15152 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15152 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15152.map.gz / Format: CCP4 / Size: 30 MB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||
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Voxel size | X=Y=Z: 10.0923 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Secreted nanoparticles (membrane vesicles, protein complexes) fro...
Entire | Name: Secreted nanoparticles (membrane vesicles, protein complexes) from Apilactobacillus kunkeei |
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Components |
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-Supramolecule #1: Secreted nanoparticles (membrane vesicles, protein complexes) fro...
Supramolecule | Name: Secreted nanoparticles (membrane vesicles, protein complexes) from Apilactobacillus kunkeei type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Apilactobacillus kunkeei (bacteria) / Strain: A1401 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Component - Concentration: 10.0 mM / Component - Name: Phosphate buffer / Details: 10 mM phosphate buffer, pH 7.4 |
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Grid | Model: Quantifoil / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot time 5s. |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: Aurion / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average exposure time: 3.0 sec. / Average electron dose: 95.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: OTHER |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Details | The initial raw movies were aligned and dose-weight filtered using alignframes from the IMOD package |
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Final reconstruction | Software - Name: IMOD (ver. v4.11.6) / Number images used: 61 |