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- EMDB-28583: CryoEM structure of GSDMB pore without transmembrane beta-barrel -

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Basic information

Entry
Database: EMDB / ID: EMD-28583
TitleCryoEM structure of GSDMB pore without transmembrane beta-barrel
Map data
Sample
  • Complex: GSDMB-pore
    • Protein or peptide: Isoform 1 of Gasdermin-B
Function / homology
Function and homology information


cytotoxic T cell pyroptotic process / wide pore channel activity / killing by host of symbiont cells / cardiolipin binding / phosphatidylinositol-4-phosphate binding / phosphatidylserine binding / pyroptosis / phosphatidylinositol-4,5-bisphosphate binding / phospholipid binding / killing of cells of another organism ...cytotoxic T cell pyroptotic process / wide pore channel activity / killing by host of symbiont cells / cardiolipin binding / phosphatidylinositol-4-phosphate binding / phosphatidylserine binding / pyroptosis / phosphatidylinositol-4,5-bisphosphate binding / phospholipid binding / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to bacterium / plasma membrane / cytoplasm
Similarity search - Function
Gasdermin, pore forming domain / Gasdermin pore forming domain / Gasdermin, PUB domain / Gasdermin PUB domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.48 Å
AuthorsWang C / Ruan J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nature / Year: 2023
Title: Structural basis for GSDMB pore formation and its targeting by IpaH7.8.
Authors: Chengliang Wang / Sonia Shivcharan / Tian Tian / Skylar Wright / Danyang Ma / JengYih Chang / Kunpeng Li / Kangkang Song / Chen Xu / Vijay A Rathinam / Jianbin Ruan /
Abstract: Gasdermins (GSDMs) are pore-forming proteins that play critical roles in host defence through pyroptosis. Among GSDMs, GSDMB is unique owing to its distinct lipid-binding profile and a lack of ...Gasdermins (GSDMs) are pore-forming proteins that play critical roles in host defence through pyroptosis. Among GSDMs, GSDMB is unique owing to its distinct lipid-binding profile and a lack of consensus on its pyroptotic potential. Recently, GSDMB was shown to exhibit direct bactericidal activity through its pore-forming activity. Shigella, an intracellular, human-adapted enteropathogen, evades this GSDMB-mediated host defence by secreting IpaH7.8, a virulence effector that triggers ubiquitination-dependent proteasomal degradation of GSDMB. Here, we report the cryogenic electron microscopy structures of human GSDMB in complex with Shigella IpaH7.8 and the GSDMB pore. The structure of the GSDMB-IpaH7.8 complex identifies a motif of three negatively charged residues in GSDMB as the structural determinant recognized by IpaH7.8. Human, but not mouse, GSDMD contains this conserved motif, explaining the species specificity of IpaH7.8. The GSDMB pore structure shows the alternative splicing-regulated interdomain linker in GSDMB as a regulator of GSDMB pore formation. GSDMB isoforms with a canonical interdomain linker exhibit normal pyroptotic activity whereas other isoforms exhibit attenuated or no pyroptotic activity. Overall, this work sheds light on the molecular mechanisms of Shigella IpaH7.8 recognition and targeting of GSDMs and shows a structural determinant in GSDMB critical for its pyroptotic activity.
History
DepositionOct 15, 2022-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateMay 3, 2023-
Current statusMay 3, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28583.png

Downloads & links

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Map

FileDownload / File: emd_28583.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.66 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.48312247 - 0.732447
Average (Standard dev.)0.0034744754 (±0.03100731)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 424.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28583_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_28583_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_28583_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GSDMB-pore

EntireName: GSDMB-pore
Components
  • Complex: GSDMB-pore
    • Protein or peptide: Isoform 1 of Gasdermin-B

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Supramolecule #1: GSDMB-pore

SupramoleculeName: GSDMB-pore / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all / Details: C24 symmetry
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform 1 of Gasdermin-B

MacromoleculeName: Isoform 1 of Gasdermin-B / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.84825 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFSVFEEITR IVVKEMDAGG DMIAVRSLVD ADRFRCFHLV GEKRTFFGCR HYTTGLTLMD ILDTDGDKWL DELDSGLQGQ KAEFQILDN VDSTGELIVR LPKEITISGS FQGFHHQKIK ISENRISQQY LATLENRKLK RELPFSFRSI NTRENLYLVT E TLETVKEE ...String:
MFSVFEEITR IVVKEMDAGG DMIAVRSLVD ADRFRCFHLV GEKRTFFGCR HYTTGLTLMD ILDTDGDKWL DELDSGLQGQ KAEFQILDN VDSTGELIVR LPKEITISGS FQGFHHQKIK ISENRISQQY LATLENRKLK RELPFSFRSI NTRENLYLVT E TLETVKEE TLKSDRQYKF WSQISQGHLS YKHKGQREVT IPPNRVLSYR VKQLVFPNKE TMSAGLDIHF RGKTKSFPEG KS LGSEDSR NMKEKLEDME SVLKDLTEEK RKDVLNSLAK CLGKEDIRQD LEQRVSEVLI SGELHMEDPD KPLLSSLFNA AGV LVEARA KAILDFLDAL LELSEEQQFV AEALEKGTLP LLKDQVKSVM EQNWDELASS PPDMDYDPEA RILCALYVVV SILL ELAEG PTSVSS

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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

Concentration0.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
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:

8efp

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41799
FSC plot (resolution estimation)

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