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Yorodumi- PDB-7wr1: P32 of caspase-4 C258A mutant in complex with OspC3 C-terminal an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wr1 | ||||||
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Title | P32 of caspase-4 C258A mutant in complex with OspC3 C-terminal ankyrin-repeat domain | ||||||
Components |
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Keywords | TRANSFERASE / ADP-riboxanase / effector / ankyrin-repeat domain | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host signal transduction pathway / modulation by symbiont of defense-related host calcium ion flux / symbiont-mediated suppression of host calcium or calmodulin-mediated signal transduction / caspase-4 / symbiont-mediated suppression of host programmed cell death / Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / non-canonical inflammasome complex assembly ...symbiont-mediated suppression of host signal transduction pathway / modulation by symbiont of defense-related host calcium ion flux / symbiont-mediated suppression of host calcium or calmodulin-mediated signal transduction / caspase-4 / symbiont-mediated suppression of host programmed cell death / Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / non-canonical inflammasome complex assembly / canonical inflammasome complex / CARD domain binding / positive regulation of tumor necrosis factor-mediated signaling pathway / cysteine-type endopeptidase activity involved in execution phase of apoptosis / pyroptotic inflammatory response / protein autoprocessing / protein maturation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Pyroptosis / intrinsic apoptotic signaling pathway / lipopolysaccharide binding / NOD1/2 Signaling Pathway / positive regulation of inflammatory response / cellular response to amyloid-beta / toxin activity / regulation of inflammatory response / regulation of apoptotic process / host cell cytoplasm / calmodulin binding / defense response to Gram-positive bacterium / defense response to bacterium / inflammatory response / cysteine-type endopeptidase activity / innate immune response / lipid binding / apoptotic process / endoplasmic reticulum membrane / endoplasmic reticulum / protein-containing complex / mitochondrion / proteolysis / extracellular region / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Shigella flexneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Hou, Y.J. / Zeng, H. / Shao, F. / Ding, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2023 Title: Structural mechanisms of calmodulin activation of Shigella effector OspC3 to ADP-riboxanate caspase-4/11 and block pyroptosis. Authors: Hou, Y. / Zeng, H. / Li, Z. / Feng, N. / Meng, F. / Xu, Y. / Li, L. / Shao, F. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wr1.cif.gz | 215.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wr1.ent.gz | 136.1 KB | Display | PDB format |
PDBx/mmJSON format | 7wr1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/7wr1 ftp://data.pdbj.org/pub/pdb/validation_reports/wr/7wr1 | HTTPS FTP |
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-Related structure data
Related structure data | 7wr0SC 7wr2C 7wr3C 7wr4C 7wr5C 7wr6C 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 32095.428 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP4 / Plasmid: pET28a-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49662, caspase-4 #2: Protein | Mass: 18366.213 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ospC3 / Plasmid: pGEX-6p-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R4X5L7 #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: 2.68 Å3/Da / Density % sol: 54.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 5% PEG8000, 0.1M Tris-HCl pH 7.5, % 2-propanol |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→46.58 Å / Num. obs: 59327 / % possible obs: 98.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 33.05 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.078 / Net I/σ(I): 17.83 |
Reflection shell | Resolution: 2.13→2.19 Å / Redundancy: 5.77 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 4.04 / Num. unique obs: 3988 / CC1/2: 0.901 / Rrim(I) all: 0.492 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7WR0 Resolution: 2.13→46.57 Å / SU ML: 0.2164 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.2496 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→46.57 Å
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Refine LS restraints |
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LS refinement shell |
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