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- EMDB-43513: Structure of a bacterial gasdermin slinky-like oligomer from a he... -

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Basic information

Entry
Database: EMDB / ID: EMD-43513
TitleStructure of a bacterial gasdermin slinky-like oligomer from a heterogeneous sample
Map databacterial gasdermin slinky-like oligomer map
Sample
  • Complex: Vitiosangium bGSDM in an active slinky-like oligomeric conformation
    • Protein or peptide: Vitiosangium bacterial gasdermin
Keywordsgasdermin / pore-forming protein / pyroptosis / bacteria / immunity / cell death / IMMUNE SYSTEM
Function / homologydefense response to virus / plasma membrane / cytoplasm / Gasdermin bGSDM
Function and homology information
Biological speciesVitiosangium sp. GDMCC 1.1324 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsJohnson AG / Mayer ML / Kranzusch PJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250-01 United States
CitationJournal: Nature / Year: 2024
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 have revealed the ...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 have revealed the functions and architectures of assemblies comprising 24 to 33 protomers, 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 more than 50 protomers. We determine a cryo-electron microscopy structure of a Vitiosangium bGSDM in an active 'slinky'-like oligomeric conformation and analyse 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
DepositionJan 25, 2024-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43513.png

Downloads & links

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Map

FileDownload / File: emd_43513.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationbacterial gasdermin slinky-like oligomer map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 680 pix.
= 904.4 Å		1.33 Å/pix.
x 680 pix.
= 904.4 Å		1.33 Å/pix.
x 680 pix.
= 904.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.33 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.34551328 - 1.0215272
Average (Standard dev.)0.000019851544 (±0.019841785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions680680680
Spacing680680680
CellA=B=C: 904.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43513_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: bacterial gasdermin slinky-like oligomer half map A

Fileemd_43513_half_map_1.map
Annotationbacterial gasdermin slinky-like oligomer half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: bacterial gasdermin slinky-like oligomer half map B

Fileemd_43513_half_map_2.map
Annotationbacterial gasdermin slinky-like oligomer half map B
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Vitiosangium bGSDM in an active slinky-like oligomeric conformation

EntireName: Vitiosangium bGSDM in an active slinky-like oligomeric conformation
Components
  • Complex: Vitiosangium bGSDM in an active slinky-like oligomeric conformation
    • Protein or peptide: Vitiosangium bacterial gasdermin

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Supramolecule #1: Vitiosangium bGSDM in an active slinky-like oligomeric conformation

SupramoleculeName: Vitiosangium bGSDM in an active slinky-like oligomeric conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vitiosangium sp. GDMCC 1.1324 (bacteria)

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Macromolecule #1: Vitiosangium bacterial gasdermin

MacromoleculeName: Vitiosangium bacterial gasdermin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Vitiosangium sp. GDMCC 1.1324 (bacteria)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMHEPES-KOH buffer (pH 7.5)
50.0 mMMethyl-6-O-(N-heptylcarbamoyl)-alpha-D-glucopyranosideHECAMEG

Details: 150 mM NaCl, 20 mM HEPES-HOH (pH 7.5), 50 mM DDMAB
GridModel: Quantifoil R1.2/1.3 / Material: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 33411 / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7n51

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 136668
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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