+Open data
-Basic information
Entry | Database: PDB / ID: 8gtj | ||||||
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Title | Crystal structure of IpaH7.8-LRR and GSDMB isoform-4 complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Complex / Effector / Pyroptosis | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host programmed cell death / cytotoxic T cell pyroptotic cell death / effector-mediated activation of programmed cell death in host / wide pore channel activity / killing by host of symbiont cells / cardiolipin binding / phosphatidylinositol-4-phosphate binding / phosphatidylserine binding / pyroptotic inflammatory response / phosphatidylinositol-4,5-bisphosphate binding ...symbiont-mediated suppression of host programmed cell death / cytotoxic T cell pyroptotic cell death / effector-mediated activation of programmed cell death in host / wide pore channel activity / killing by host of symbiont cells / cardiolipin binding / phosphatidylinositol-4-phosphate binding / phosphatidylserine binding / pyroptotic inflammatory response / phosphatidylinositol-4,5-bisphosphate binding / RING-type E3 ubiquitin transferase / phospholipid binding / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / killing of cells of another organism / defense response to Gram-negative bacterium / host cell cytoplasm / protein ubiquitination / defense response to bacterium / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Shigella flexneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Zhong, X. / Hou, Y.J. / Ding, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Nature / Year: 2023 Title: Structural mechanisms for regulation of GSDMB pore-forming activity. Authors: Xiu Zhong / Huan Zeng / Zhiwei Zhou / Ya Su / Hang Cheng / Yanjie Hou / Yang She / Na Feng / Jia Wang / Feng Shao / Jingjin Ding / Abstract: Cytotoxic lymphocyte-derived granzyme A (GZMA) cleaves GSDMB, a gasdermin-family pore-forming protein, to trigger target cell pyroptosis. GSDMB and the charter gasdermin family member GSDMD have been ...Cytotoxic lymphocyte-derived granzyme A (GZMA) cleaves GSDMB, a gasdermin-family pore-forming protein, to trigger target cell pyroptosis. GSDMB and the charter gasdermin family member GSDMD have been inconsistently reported to be degraded by the Shigella flexneri ubiquitin-ligase virulence factor IpaH7.8 (refs. ). Whether and how IpaH7.8 targets both gasdermins is undefined, and the pyroptosis function of GSDMB has even been questioned recently. Here we report the crystal structure of the IpaH7.8-GSDMB complex, which shows how IpaH7.8 recognizes the GSDMB pore-forming domain. We clarify that IpaH7.8 targets human (but not mouse) GSDMD through a similar mechanism. The structure of full-length GSDMB suggests stronger autoinhibition than in other gasdermins. GSDMB has multiple splicing isoforms that are equally targeted by IpaH7.8 but exhibit contrasting pyroptotic activities. Presence of exon 6 in the isoforms dictates the pore-forming, pyroptotic activity in GSDMB. We determine the cryo-electron microscopy structure of the 27-fold-symmetric GSDMB pore and depict conformational changes that drive pore formation. The structure uncovers an essential role for exon-6-derived elements in pore assembly, explaining pyroptosis deficiency in the non-canonical splicing isoform used in recent studies. Different cancer cell lines have markedly different isoform compositions, correlating with the onset and extent of pyroptosis following GZMA stimulation. Our study illustrates fine regulation of GSDMB pore-forming activity by pathogenic bacteria and mRNA splicing and defines the underlying structural mechanisms. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gtj.cif.gz | 270 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gtj.ent.gz | 198.2 KB | Display | PDB format |
PDBx/mmJSON format | 8gtj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/8gtj ftp://data.pdbj.org/pub/pdb/validation_reports/gt/8gtj | HTTPS FTP |
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-Related structure data
Related structure data | 8gtkC 8gtnC 3cvrS 5tj2S S: Starting model for refinement 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 47128.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSDMB, GSDML, PP4052, PRO2521 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8TAX9 #2: Protein | Mass: 27840.521 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaH7.8, CP0078, pWR501_0084, SFLP133 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P18014, RING-type E3 ubiquitin transferase #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 1.2 M Sodium potassium phosphate |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 42928 / % possible obs: 99.9 % / Redundancy: 18.4 % / Biso Wilson estimate: 60.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rrim(I) all: 0.1 / Net I/σ(I): 26.13 |
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 19.6 % / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 3.34 / Num. unique obs: 3147 / CC1/2: 0.894 / Rrim(I) all: 0.875 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TJ2, 3CVR Resolution: 2.7→45.15 Å / SU ML: 0.442 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.4089 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→45.15 Å
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Refine LS restraints |
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LS refinement shell |
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