+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43509 | |||||||||
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Title | Structure of a bacterial gasdermin medium oval pore assembly | |||||||||
Map data | ~40mer oval pore map | |||||||||
Sample |
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Keywords | gasdermin / pore-forming protein / pyroptosis / bacteria / immunity / cell death / IMMUNE SYSTEM | |||||||||
Function / homology | defense response to virus / plasma membrane / cytoplasm / Gasdermin bGSDM Function and homology information | |||||||||
Biological species | Vitiosangium sp. GDMCC 1.1324 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.6 Å | |||||||||
Authors | Johnson AG / Mayer ML / Kranzusch PJ | |||||||||
Funding support | United States, 1 items
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Citation | Journal: bioRxiv / Year: 2023 Title: Structure and assembly of a bacterial gasdermin pore. Authors: Alex G Johnson / Megan L Mayer / Stefan L Schaefer / Nora K McNamara-Bordewick / Gerhard Hummer / Philip J Kranzusch / Abstract: In response to pathogen infection, gasdermin (GSDM) proteins form membrane pores that induce a host cell death process called pyroptosis. Studies of human and mouse GSDM pores reveal the functions ...In response to pathogen infection, gasdermin (GSDM) proteins form membrane pores that induce a host cell death process called pyroptosis. Studies of human and mouse GSDM pores reveal the functions and architectures of 24-33 protomers assemblies, but the mechanism and evolutionary origin of membrane targeting and GSDM pore formation remain unknown. Here we determine a structure of a bacterial GSDM (bGSDM) pore and define a conserved mechanism of pore assembly. Engineering a panel of bGSDMs for site-specific proteolytic activation, we demonstrate that diverse bGSDMs form distinct pore sizes that range from smaller mammalian-like assemblies to exceptionally large pores containing >50 protomers. We determine a 3.3 Å cryo-EM structure of a bGSDM in an active slinky-like oligomeric conformation and analyze bGSDM pores in a native lipid environment to create an atomic-level model of a full 52-mer bGSDM pore. Combining our structural analysis with molecular dynamics simulations and cellular assays, our results support a stepwise model of GSDM pore assembly and suggest that a covalently bound palmitoyl can leave a hydrophobic sheath and insert into the membrane before formation of the membrane-spanning β-strand regions. These results reveal the diversity of GSDM pores found in nature and explain the function of an ancient post-translational modification in enabling programmed host cell death. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43509.map.gz | 75.6 MB | EMDB map data format | |
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Header (meta data) | emd-43509-v30.xml emd-43509.xml | 16.5 KB 16.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_43509_fsc.xml | 11.2 KB | Display | FSC data file |
Images | emd_43509.png | 42.2 KB | ||
Masks | emd_43509_msk_1.map | 149.9 MB | Mask map | |
Filedesc metadata | emd-43509.cif.gz | 5.1 KB | ||
Others | emd_43509_half_map_1.map.gz emd_43509_half_map_2.map.gz | 139.1 MB 139.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43509 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43509 | HTTPS FTP |
-Validation report
Summary document | emd_43509_validation.pdf.gz | 810.5 KB | Display | EMDB validaton report |
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Full document | emd_43509_full_validation.pdf.gz | 810.1 KB | Display | |
Data in XML | emd_43509_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | emd_43509_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43509 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43509 | HTTPS FTP |
-Related structure data
Related structure data | 8sl0C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_43509.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | ~40mer oval pore map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.66 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_43509_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: ~40mer oval pore half map B
File | emd_43509_half_map_1.map | ||||||||||||
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Annotation | ~40mer oval pore half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: ~40mer oval pore half map B
File | emd_43509_half_map_2.map | ||||||||||||
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Annotation | ~40mer oval pore half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Vitiosangium bGSDM in an medium oval pore assembly
Entire | Name: Vitiosangium bGSDM in an medium oval pore assembly |
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Components |
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-Supramolecule #1: Vitiosangium bGSDM in an medium oval pore assembly
Supramolecule | Name: Vitiosangium bGSDM in an medium oval pore assembly / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Vitiosangium sp. GDMCC 1.1324 (bacteria) |
-Macromolecule #1: Vitiosangium bacterial gasdermin
Macromolecule | Name: Vitiosangium bacterial gasdermin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Vitiosangium sp. GDMCC 1.1324 (bacteria) |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: SGLCSDPAIT YLKRLGYNVV RLPREGIQPL HLLGQQRGTV EYLGSLEKLI TQPPSEPPAI TRDQAAAGIN GQKTENLSFS IGINILKSVL AQFGAGAGIE AQYNQARKVR FEFSNVLADS VEPLAVGQFL KMAEVDADNP VLKQYVLGNG RLYVITQVIK SNEFTVAAEK ...String: SGLCSDPAIT YLKRLGYNVV RLPREGIQPL HLLGQQRGTV EYLGSLEKLI TQPPSEPPAI TRDQAAAGIN GQKTENLSFS IGINILKSVL AQFGAGAGIE AQYNQARKVR FEFSNVLADS VEPLAVGQFL KMAEVDADNP VLKQYVLGNG RLYVITQVIK SNEFTVAAEK SGGGSIQLDV PEIQKVVGGK LKVEASVSSQ STVTYKGEKQ LVFGFKCFEI GVKNGEITLF ASQLVPR UniProtKB: Gasdermin bGSDM |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
Details: 150 mM NaCl, 20 mM HEPES-HOH (pH 7.5), 50 mM HECAMEG | ||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2 | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | The sample was monodisperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 33411 / Average electron dose: 53.0 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: 2.8000000000000003 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |