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Yorodumi- EMDB-13585: Cryo-electron tomography of ASC signalling sites in pyroptotic cells -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13585 | |||||||||
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Title | Cryo-electron tomography of ASC signalling sites in pyroptotic cells | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Mus musculus (house mouse) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Liu Y / Zhai H / Alemayehu H / Hopkins LJ / Borgeaud AC / Heroven C / Howe JD / Boulanger J / Bryant CE / Modis Y | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: To Be Published Title: Cryo-electron tomography of ASC signalling sites in pyroptotic cells Authors: Liu Y / Zhai H / Alemayehu H / Hopkins LJ / Borgeaud AC / Heroven C / Howe JD / Boulanger J / Bryant CE / Modis Y | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13585.map.gz | 704.8 MB | EMDB map data format | |
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Header (meta data) | emd-13585-v30.xml emd-13585.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
Images | emd_13585.png | 190.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13585 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13585 | HTTPS FTP |
-Validation report
Summary document | emd_13585_validation.pdf.gz | 397.9 KB | Display | EMDB validaton report |
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Full document | emd_13585_full_validation.pdf.gz | 397.4 KB | Display | |
Data in XML | emd_13585_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | emd_13585_validation.cif.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13585 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13585 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13585.map.gz / Format: CCP4 / Size: 760.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 13.58 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : FIB milled iBMDMs
Entire | Name: FIB milled iBMDMs |
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Components |
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-Supramolecule #1: FIB milled iBMDMs
Supramolecule | Name: FIB milled iBMDMs / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 Details: DMEM medium supplemented with 10% heat-inactivated FBS (Gibco) |
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: LEICA EM GP |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 1 nA / Focused ion beam - Duration: 1500 sec. / Focused ion beam - Temperature: 83 K / Focused ion beam - Initial thickness: 10000 nm / Focused ion beam - Final thickness: 200 nm Focused ion beam - Details: Lamella were made using a Scios DualBeam FIB/SEM (FEI) equipped with a Quorum cryo-stage (PP3010T). Rough milling was performed using 0.5 to 0.1 nA current. Fine milling ...Focused ion beam - Details: Lamella were made using a Scios DualBeam FIB/SEM (FEI) equipped with a Quorum cryo-stage (PP3010T). Rough milling was performed using 0.5 to 0.1 nA current. Fine milling was done using 50 to 10 pA current.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 121 / Average electron dose: 1.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 7.0 µm / Nominal defocus min: 4.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution method: OTHER / Software - Name: eTomo / Number images used: 100 |
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CTF correction | Software - Name: eTomo (ver. 4.10.20) |