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Open data
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Basic information
Entry | Database: PDB / ID: 6kn0 | ||||||
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Title | caspase-1 P20/P10 C285A in complex with human GSDMD-C domain | ||||||
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![]() | IMMUNE SYSTEM / pyroptosis | ||||||
Function / homology | ![]() caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / pore complex assembly / The IPAF inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / icosanoid biosynthetic process / NLRP1 inflammasome complex ...caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / pore complex assembly / The IPAF inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / icosanoid biosynthetic process / NLRP1 inflammasome complex / cytokine precursor processing / canonical inflammasome complex / positive regulation of interleukin-18 production / : / Release of apoptotic factors from the mitochondria / wide pore channel activity / NLRP3 inflammasome complex / CARD domain binding / caspase binding / cardiolipin binding / Regulation of TLR by endogenous ligand / phosphatidic acid binding / positive regulation of tumor necrosis factor-mediated signaling pathway / Interleukin-1 processing / osmosensory signaling pathway / Interleukin-37 signaling / phosphatidylinositol-4-phosphate binding / pattern recognition receptor signaling pathway / : / signaling receptor ligand precursor processing / TP53 Regulates Transcription of Caspase Activators and Caspases / phosphatidylserine binding / pyroptotic inflammatory response / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / The NLRP3 inflammasome / protein autoprocessing / protein maturation / protein secretion / Pyroptosis / Purinergic signaling in leishmaniasis infection / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of interleukin-1 beta production / mitochondrial membrane / NOD1/2 Signaling Pathway / protein homooligomerization / kinase binding / cellular response to type II interferon / positive regulation of inflammatory response / cellular response to mechanical stimulus / specific granule lumen / SARS-CoV-1 activates/modulates innate immune responses / tertiary granule lumen / regulation of inflammatory response / cellular response to lipopolysaccharide / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / microtubule / defense response to virus / endopeptidase activity / ficolin-1-rich granule lumen / defense response to Gram-positive bacterium / defense response to bacterium / inflammatory response / cysteine-type endopeptidase activity / innate immune response / apoptotic process / Neutrophil degranulation / nucleolus / signal transduction / protein-containing complex / proteolysis / extracellular space / extracellular region / nucleoplasm / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ding, J. / Sun, Q. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 181.6 KB | Display | ![]() |
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PDB format | ![]() | 144.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.1 KB | Display | ![]() |
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Full document | ![]() | 484.6 KB | Display | |
Data in XML | ![]() | 31.6 KB | Display | |
Data in CIF | ![]() | 42.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kmtC ![]() 6kmuSC ![]() 6kmvC ![]() 6kmzC ![]() 6kn1C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18778.658 Da / Num. of mol.: 2 / Mutation: C285A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 10258.755 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 21250.285 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 150 mM KBr, 30% (w/v) polyethylene glycol mono-methyester 2000 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→47.45 Å / Num. obs: 21818 / % possible obs: 97 % / Redundancy: 3.32 % / CC1/2: 0.993 / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.79→2.87 Å / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 1526 / CC1/2: 0.876 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6KMU Resolution: 2.793→47.447 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.793→47.447 Å
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LS refinement shell | Resolution: 2.7931→2.8629 Å
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