+Open data
-Basic information
Entry | Database: PDB / ID: 6kmu | ||||||
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Title | P22/P10 complex of caspase-11 mutant C254A | ||||||
Components | (Caspase-4) x 5 | ||||||
Keywords | IMMUNE SYSTEM / pyroptosis | ||||||
Function / homology | Function and homology information caspase-11 / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / Pyroptosis / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / NLRP1 inflammasome complex / NOD1/2 Signaling Pathway / positive regulation of macrophage cytokine production / positive regulation of NLRP3 inflammasome complex assembly ...caspase-11 / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / Pyroptosis / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / NLRP1 inflammasome complex / NOD1/2 Signaling Pathway / positive regulation of macrophage cytokine production / positive regulation of NLRP3 inflammasome complex assembly / pyroptotic inflammatory response / protein autoprocessing / protein maturation / ectopic germ cell programmed cell death / positive regulation of interleukin-1 beta production / actin filament organization / lipopolysaccharide binding / positive regulation of inflammatory response / positive regulation of neuron apoptotic process / regulation of inflammatory response / scaffold protein binding / defense response to Gram-positive bacterium / defense response to bacterium / inflammatory response / cysteine-type endopeptidase activity / innate immune response / neuronal cell body / lipid binding / endoplasmic reticulum membrane / protein-containing complex / mitochondrion / extracellular region / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Ding, J. / Sun, Q. | ||||||
Citation | Journal: Cell / Year: 2020 Title: Structural Mechanism for GSDMD Targeting by Autoprocessed Caspases in Pyroptosis. Authors: Wang, K. / Sun, Q. / Zhong, X. / Zeng, M. / Zeng, H. / Shi, X. / Li, Z. / Wang, Y. / Zhao, Q. / 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 | 6kmu.cif.gz | 217.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kmu.ent.gz | 172 KB | Display | PDB format |
PDBx/mmJSON format | 6kmu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/6kmu ftp://data.pdbj.org/pub/pdb/validation_reports/km/6kmu | HTTPS FTP |
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-Related structure data
Related structure data | 6kmtSC 6kmvC 6kmzC 6kn0C 6kn1C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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
-Protein , 5 types, 8 molecules AEBFHCDG
#1: Protein | Mass: 20783.809 Da / Num. of mol.: 2 / Mutation: C254A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Casp4, Casp11, Caspl, Ich3 / Plasmid: pSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P70343, caspase-11 #2: Protein | Mass: 10113.619 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Casp4, Casp11, Caspl, Ich3 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P70343, caspase-11 #3: Protein | | Mass: 20884.914 Da / Num. of mol.: 1 / Mutation: C254A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Casp4, Casp11, Caspl, Ich3 / Plasmid: pSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P70343, caspase-11 #4: Protein | | Mass: 10212.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Casp4, Casp11, Caspl, Ich3 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P70343, caspase-11 #5: Protein | | Mass: 17408.006 Da / Num. of mol.: 1 / Mutation: C254A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Casp4, Casp11, Caspl, Ich3 / Plasmid: pSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P70343, caspase-11 |
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-Non-polymers , 1 types, 364 molecules
#6: 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: 2.74 Å3/Da / Density % sol: 55.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM HEPES (pH 7.5), 12% (w/v) polyethylene glycol 3350, and 4% formaldehyde |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97892 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97892 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→49.78 Å / Num. obs: 71527 / % possible obs: 97.7 % / Redundancy: 3.41 % / CC1/2: 0.997 / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.81 |
Reflection shell | Resolution: 2.1→2.15 Å / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.72 / Num. unique obs: 5274 / CC1/2: 0.915 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6kmt Resolution: 2.1→49.78 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.1→49.78 Å
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LS refinement shell | Resolution: 2.0994→2.1519 Å
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