+Open data
-Basic information
Entry | Database: PDB / ID: 7wjq | ||||||
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Title | Crystal structure of GSDMB in complex with Ipah7.8 | ||||||
Components |
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Keywords | ANTIVIRAL PROTEIN | ||||||
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 / programmed cell death / cardiolipin binding / phosphatidylinositol-4-phosphate binding / pyroptotic inflammatory response / phosphatidylserine 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 / programmed cell death / cardiolipin binding / phosphatidylinositol-4-phosphate binding / pyroptotic inflammatory response / phosphatidylserine binding / phosphatidylinositol-4,5-bisphosphate binding / RING-type E3 ubiquitin transferase / phospholipid binding / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / defense response to Gram-negative bacterium / host cell cytoplasm / killing of cells of another organism / protein ubiquitination / defense response to bacterium / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Shigella flexneri (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Li, X. / Zhang, H. / Yin, H. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Insights into the GSDMB-mediated cellular lysis and its targeting by IpaH7.8 Authors: Yin, H. / Zheng, J. / He, Q. / Zhang, X. / Li, X. / Ma, Y. / Liang, X. / Gao, J. / Kocsis, B.L. / Li, Z. / Liu, X. / Alto, N.M. / Li, L. / Zhang, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wjq.cif.gz | 286.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wjq.ent.gz | 190.5 KB | Display | PDB format |
PDBx/mmJSON format | 7wjq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wjq_validation.pdf.gz | 435.9 KB | Display | wwPDB validaton report |
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Full document | 7wjq_full_validation.pdf.gz | 440.3 KB | Display | |
Data in XML | 7wjq_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 7wjq_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/7wjq ftp://data.pdbj.org/pub/pdb/validation_reports/wj/7wjq | HTTPS FTP |
-Related structure data
Related structure data | 5tj4S S: Starting model for refinement |
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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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Unit cell |
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-Components
#1: Protein | Mass: 27895.385 Da / Num. of mol.: 1 / Mutation: M262D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: P18014, RING-type E3 ubiquitin transferase |
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#2: Protein | Mass: 44482.590 Da / Num. of mol.: 1 / Mutation: R221S, K222A 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 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.86 % |
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Crystal grow | Temperature: 291.15 K / Method: liquid diffusion Details: NaCl, HEPES sodium, PEG 8000, ammonium sulfate, 1,6-hexanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→66.67 Å / Num. obs: 17543 / % possible obs: 97 % / Redundancy: 10.7 % / Biso Wilson estimate: 47.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.7→2.83 Å / Num. unique obs: 2254 / CC1/2: 0.967 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TJ4 Resolution: 2.7→48.43 Å / SU ML: 0.2498 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4956 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: 53.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→48.43 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -26.7751240815 Å / Origin y: 5.07059930869 Å / Origin z: 12.2707426571 Å
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Refinement TLS group | Selection details: all |