+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44035 | |||||||||
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Title | Full-length GSDMD | |||||||||
Map data | Full-length GSDMD, no sharp | |||||||||
Sample |
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Keywords | Gasdermin D / pyroptosis / inflammasome / palmitoylation / pore formation / IMMUNE SYSTEM | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.22 Å | |||||||||
Authors | Hao W / Gang D | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature Title: ROS-dependent S-palmitoylation activates pore formation by cleaved and intact GSDMD Authors: Gang D / Liam B / Hao W | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_44035.map.gz | 15.1 MB | EMDB map data format | |
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Header (meta data) | emd-44035-v30.xml emd-44035.xml | 13.4 KB 13.4 KB | Display Display | EMDB header |
Images | emd_44035.png | 54.8 KB | ||
Filedesc metadata | emd-44035.cif.gz | 3.6 KB | ||
Others | emd_44035_additional_1.map.gz emd_44035_half_map_1.map.gz emd_44035_half_map_2.map.gz | 28.6 MB 28.3 MB 28.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44035 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44035 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_44035.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Full-length GSDMD, no sharp | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.41 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Full-length GSDMD, sharp
File | emd_44035_additional_1.map | ||||||||||||
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Annotation | Full-length GSDMD, sharp | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_44035_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_44035_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Full-length GSDMD
Entire | Name: Full-length GSDMD |
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Components |
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-Supramolecule #1: Full-length GSDMD
Supramolecule | Name: Full-length GSDMD / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.2 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
Details | This sample is Full-length GSDMD |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.238 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 239554 |