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- EMDB-43509: Structure of a bacterial gasdermin medium oval pore assembly -

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Basic information

Entry
Database: EMDB / ID: EMD-43509
TitleStructure of a bacterial gasdermin medium oval pore assembly
Map data~40mer oval pore map
Sample
  • Complex: Vitiosangium bGSDM in an medium oval pore assembly
    • 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: 6.6 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: 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
DepositionJan 25, 2024-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43509.png

Downloads & links

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Map

FileDownload / File: emd_43509.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation~40mer oval pore map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.66 Å/pix.
x 340 pix.
= 904.4 Å		2.66 Å/pix.
x 340 pix.
= 904.4 Å		2.66 Å/pix.
x 340 pix.
= 904.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-0.36285755 - 1.689671
Average (Standard dev.)-0.0003205255 (±0.04382351)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 904.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43509_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ~40mer oval pore half map B

Fileemd_43509_half_map_1.map
Annotation~40mer oval pore half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ~40mer oval pore half map B

Fileemd_43509_half_map_2.map
Annotation~40mer oval pore half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Vitiosangium bGSDM in an medium oval pore assembly

EntireName: Vitiosangium bGSDM in an medium oval pore assembly
Components
  • Complex: Vitiosangium bGSDM in an medium oval pore assembly
    • Protein or peptide: Vitiosangium bacterial gasdermin

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Supramolecule #1: Vitiosangium bGSDM in an medium oval pore assembly

SupramoleculeName: Vitiosangium bGSDM in an medium oval pore assembly / 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 stateparticle

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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 HECAMEG
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2
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: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39527
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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