+Open data
-Basic information
Entry | Database: PDB / ID: 8et2 | ||||||
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Title | CryoEM structure of the GSDMB pore | ||||||
Components | Isoform 1 of Gasdermin-B | ||||||
Keywords | IMMUNE SYSTEM / Pore-forming protein / GSDMB / pyroptosis | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.96 Å | ||||||
Authors | Wang, C. / Ruan, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8et2.cif.gz | 969.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8et2.ent.gz | 800.7 KB | Display | PDB format |
PDBx/mmJSON format | 8et2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/8et2 ftp://data.pdbj.org/pub/pdb/validation_reports/et/8et2 | HTTPS FTP |
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-Related structure data
Related structure data | 28584MC 8efpC 8et1C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 46848.250 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSDMB, GSDML, PP4052, PRO2521 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TAX9 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: GSDMB-pore / Type: COMPLEX / Details: C24 symmetry / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: DIFFRACTION / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: SerialEM / Category: image acquisition | ||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41799 / Symmetry type: POINT | ||||||||||||||||||||||||
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