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- EMDB-28584: CryoEM structure of the GSDMB pore -

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Basic information

Entry
Database: EMDB / ID: EMD-28584
TitleCryoEM structure of the GSDMB pore
Map data
Sample
  • Complex: GSDMB-pore
    • Protein or peptide: Isoform 1 of Gasdermin-B
KeywordsPore-forming protein / GSDMB / pyroptosis / IMMUNE SYSTEM
Function / homology
Function and homology information


cytotoxic T cell pyroptotic cell death / wide pore channel activity / killing by host of symbiont cells / programmed cell death / cardiolipin binding / phosphatidylinositol-4-phosphate binding / pyroptotic inflammatory response / phosphatidylserine binding / phosphatidylinositol-4,5-bisphosphate binding / phospholipid binding ...cytotoxic T cell pyroptotic cell death / wide pore channel activity / killing by host of symbiont cells / programmed cell death / cardiolipin binding / phosphatidylinositol-4-phosphate binding / pyroptotic inflammatory response / phosphatidylserine binding / phosphatidylinositol-4,5-bisphosphate binding / phospholipid binding / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to bacterium / plasma membrane / cytoplasm
Similarity search - Function
Gasdermin, PUB domain / Gasdermin PUB domain / Gasdermin, pore forming domain / Gasdermin pore forming domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.96 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-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28584.png

Downloads & links

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Map

FileDownload / File: emd_28584.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 256 pix.
= 424.96 Å		1.66 Å/pix.
x 256 pix.
= 424.96 Å		1.66 Å/pix.
x 256 pix.
= 424.96 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.7164639 - 1.058364
Average (Standard dev.)0.0035256918 (±0.03597003)
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_28584_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_28584_half_map_1.map
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Half map: #1

Fileemd_28584_half_map_2.map
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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 / 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

UniProtKB: Gasdermin-B

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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 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
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
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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41799
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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