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- PDB-7wr6: Crystal structure of ADP-riboxanated caspase-4 in complex with Af1521 -
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Open data
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Basic information
Entry | Database: PDB / ID: 7wr6 | ||||||
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Title | Crystal structure of ADP-riboxanated caspase-4 in complex with Af1521 | ||||||
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![]() | HYDROLASE / ADP-riboxanation | ||||||
Function / homology | ![]() caspase-4 / non-canonical inflammasome complex / ADP-ribosylglutamate hydrolase activity / positive regulation of interleukin-18-mediated signaling pathway / peptidyl-glutamate ADP-deribosylation / non-canonical inflammasome complex assembly / AIM2 inflammasome complex / IPAF inflammasome complex / NLRP1 inflammasome complex / NLRP3 inflammasome complex ...caspase-4 / non-canonical inflammasome complex / ADP-ribosylglutamate hydrolase activity / positive regulation of interleukin-18-mediated signaling pathway / peptidyl-glutamate ADP-deribosylation / non-canonical inflammasome complex assembly / AIM2 inflammasome complex / IPAF inflammasome complex / NLRP1 inflammasome complex / NLRP3 inflammasome complex / CARD domain binding / caspase binding / positive regulation of tumor necrosis factor-mediated signaling pathway / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / 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 / positive regulation of neuron apoptotic process / regulation of inflammatory response / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hou, Y.J. / Zeng, H. / Shao, F. / Ding, J. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.3 KB | Display | ![]() |
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PDB format | ![]() | 80.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 823.6 KB | Display | ![]() |
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Full document | ![]() | 829.1 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 28.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wr0SC ![]() 7wr1C ![]() 7wr2C ![]() 7wr3C ![]() 7wr4C ![]() 7wr5C ![]() 2bfqS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32095.428 Da / Num. of mol.: 1 / Mutation: C258A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 21706.051 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16 Gene: AF_1521 / Plasmid: pGEX-6p-2 / Production host: ![]() ![]() References: UniProt: O28751, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
#3: Chemical | ChemComp-5ZY / [[( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 27% PEG 3350, 0.05M CAPSO pH 9.0 |
-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: 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: 1.96→38.45 Å / Num. obs: 34358 / % possible obs: 97.7 % / Redundancy: 12.88 % / Biso Wilson estimate: 34.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.064 / Net I/σ(I): 24.49 |
Reflection shell | Resolution: 1.96→2.01 Å / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 3.92 / Num. unique obs: 2364 / CC1/2: 0.936 / Rrim(I) all: 0.69 / % possible all: 92 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2BFQ, 7WR0 Resolution: 1.96→38.45 Å / SU ML: 0.2302 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.7199 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: 43.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→38.45 Å
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Refine LS restraints |
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LS refinement shell |
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