+Open data
-Basic information
Entry | Database: PDB / ID: 6cb8 | ||||||||||||
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Title | Cryo-EM structure of the Gasdermin A3 membrane pore | ||||||||||||
Components | Gasdermin-A3 | ||||||||||||
Keywords | IMMUNE SYSTEM / Pyroptosis / Pore forming protein | ||||||||||||
Function / homology | Function and homology information sebaceous gland cell differentiation / avascular cornea development in camera-type eye / negative regulation of timing of anagen / hair cycle / wide pore channel activity / mammary gland development / positive regulation of extrinsic apoptotic signaling pathway / phosphatidylinositol-4-phosphate binding / hair follicle development / skin development ...sebaceous gland cell differentiation / avascular cornea development in camera-type eye / negative regulation of timing of anagen / hair cycle / wide pore channel activity / mammary gland development / positive regulation of extrinsic apoptotic signaling pathway / phosphatidylinositol-4-phosphate binding / hair follicle development / skin development / hair follicle morphogenesis / phosphatidylserine binding / pyroptotic inflammatory response / somatic stem cell population maintenance / extrinsic apoptotic signaling pathway / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of interleukin-1 beta production / negative regulation of canonical Wnt signaling pathway / mitochondrial membrane / defense response to bacterium / positive regulation of apoptotic process / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Ruan, J. / Wu, H. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nature / Year: 2018 Title: Cryo-EM structure of the gasdermin A3 membrane pore. Authors: Jianbin Ruan / Shiyu Xia / Xing Liu / Judy Lieberman / Hao Wu / Abstract: Gasdermins mediate inflammatory cell death after cleavage by caspases or other, unknown enzymes. The cleaved N-terminal fragments bind to acidic membrane lipids to form pores, but the mechanism of ...Gasdermins mediate inflammatory cell death after cleavage by caspases or other, unknown enzymes. The cleaved N-terminal fragments bind to acidic membrane lipids to form pores, but the mechanism of pore formation remains unresolved. Here we present the cryo-electron microscopy structures of the 27-fold and 28-fold single-ring pores formed by the N-terminal fragment of mouse GSDMA3 (GSDMA3-NT) at 3.8 and 4.2 Å resolutions, and of a double-ring pore at 4.6 Å resolution. In the 27-fold pore, a 108-stranded anti-parallel β-barrel is formed by two β-hairpins from each subunit capped by a globular domain. We identify a positively charged helix that interacts with the acidic lipid cardiolipin. GSDMA3-NT undergoes radical conformational changes upon membrane insertion to form long, membrane-spanning β-strands. We also observe an unexpected additional symmetric ring of GSDMA3-NT subunits that does not insert into the membrane in the double-ring pore, which may represent a pre-pore state of GSDMA3-NT. These structures provide a basis that explains the activities of several mutant gasdermins, including defective mutants that are associated with cancer. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6cb8.cif.gz | 106.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cb8.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 6cb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cb8_validation.pdf.gz | 773.5 KB | Display | wwPDB validaton report |
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Full document | 6cb8_full_validation.pdf.gz | 779.2 KB | Display | |
Data in XML | 6cb8_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 6cb8_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/6cb8 ftp://data.pdbj.org/pub/pdb/validation_reports/cb/6cb8 | HTTPS FTP |
-Related structure data
Related structure data | 7449MC 7450C 7451C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: C27 (27 fold cyclic)) |
-Components
#1: Protein | Mass: 30401.035 Da / Num. of mol.: 1 / Fragment: residues 1-262 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsdma3, Gsdm3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5Y4Y6 |
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#2: Chemical | ChemComp-CDL / |
-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: Gasdermin A3 N domain / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.81 MDa / Experimental value: NO |
Source (natural) | Organism: Mus musculus (house mouse) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: (1.12_2829: ???) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||
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EM software | Name: RELION / Version: 2 / Category: 3D reconstruction | ||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C27 (27 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40086 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.8→57.261 Å / SU ML: 0.56 / σ(F): 0.12 / Phase error: 39.43 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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LS refinement shell |
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