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Yorodumi- EMDB-43513: Structure of a bacterial gasdermin slinky-like oligomer from a he... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43513 | |||||||||
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Title | Structure of a bacterial gasdermin slinky-like oligomer from a heterogeneous sample | |||||||||
Map data | bacterial gasdermin slinky-like oligomer 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: 4.0 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_43513.map.gz | 602.1 MB | EMDB map data format | |
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Header (meta data) | emd-43513-v30.xml emd-43513.xml | 14.9 KB 14.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_43513_fsc.xml | 22.5 KB | Display | FSC data file |
Images | emd_43513.png | 68.1 KB | ||
Masks | emd_43513_msk_1.map | 1.2 GB | Mask map | |
Filedesc metadata | emd-43513.cif.gz | 5 KB | ||
Others | emd_43513_half_map_1.map.gz emd_43513_half_map_2.map.gz | 1.1 GB 1.1 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43513 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43513 | HTTPS FTP |
-Related structure data
Related structure data | 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_43513.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | bacterial gasdermin slinky-like oligomer map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.33 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_43513_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: bacterial gasdermin slinky-like oligomer half map A
File | emd_43513_half_map_1.map | ||||||||||||
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Annotation | bacterial gasdermin slinky-like oligomer half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: bacterial gasdermin slinky-like oligomer half map B
File | emd_43513_half_map_2.map | ||||||||||||
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Annotation | bacterial gasdermin slinky-like oligomer half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Vitiosangium bGSDM in an active slinky-like oligomeric conformation
Entire | Name: Vitiosangium bGSDM in an active slinky-like oligomeric conformation |
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Components |
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-Supramolecule #1: Vitiosangium bGSDM in an active slinky-like oligomeric conformation
Supramolecule | Name: Vitiosangium bGSDM in an active slinky-like oligomeric conformation 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 | filament |
-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 DDMAB | ||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD | ||||||||||||
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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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: 2.8000000000000003 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 33411 / Average electron dose: 53.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |