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- PDB-1ibc: CRYSTAL STRUCTURE OF INHIBITED INTERLEUKIN-1BETA CONVERTING ENZYME -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ibc | ||||||
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Title | CRYSTAL STRUCTURE OF INHIBITED INTERLEUKIN-1BETA CONVERTING ENZYME | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / PROTEASE / CYSTEINE PROTEASE / INTERLEUKIN-1BETA CONVERTING ENZYME / ICE / CASPASE-1 / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / The IPAF inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / icosanoid biosynthetic process / NLRP1 inflammasome complex / cytokine precursor processing ...caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / 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 / NLRP3 inflammasome complex / CARD domain binding / caspase binding / positive regulation of tumor necrosis factor-mediated signaling pathway / Interleukin-1 processing / osmosensory signaling pathway / Interleukin-37 signaling / pattern recognition receptor signaling pathway / : / signaling receptor ligand precursor processing / TP53 Regulates Transcription of Caspase Activators and Caspases / 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 / Pyroptosis / Purinergic signaling in leishmaniasis infection / positive regulation of interleukin-1 beta production / NOD1/2 Signaling Pathway / kinase binding / cellular response to type II interferon / positive regulation of inflammatory response / cellular response to mechanical stimulus / SARS-CoV-1 activates/modulates innate immune responses / regulation of inflammatory response / cellular response to lipopolysaccharide / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / microtubule / defense response to virus / endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / nucleolus / signal transduction / protein-containing complex / proteolysis / identical protein binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Becker, J.W. / Rotonda, J. | ||||||
![]() | ![]() Title: A combinatorial approach for determining protease specificities: application to interleukin-1beta converting enzyme (ICE). Authors: Rano, T.A. / Timkey, T. / Peterson, E.P. / Rotonda, J. / Nicholson, D.W. / Becker, J.W. / Chapman, K.T. / Thornberry, N.A. #1: ![]() Title: Interleukin-1 Beta Converting Enzyme: A Novel Cysteine Protease Required for Il-1 Beta Production and Implicated in Programmed Cell Death Authors: Thornberry, N.A. / Molineaux, S.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.3 KB | Display | ![]() |
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PDB format | ![]() | 49.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.8 KB | Display | ![]() |
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Full document | ![]() | 438.3 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 15.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 21482.574 Da / Num. of mol.: 1 / Mutation: D381A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 10214.745 Da / Num. of mol.: 1 / Mutation: D381A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 596.611 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 58 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: 1.5 ML DROPS OF PROTEIN-INHIBITOR SOLUTION (5.0 MG/ML IN 10 MILLIMOLAR TRIS-HCL, PH 8.5, 10 MILLI-MOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) WERE MIXED WITH AN EQUAL VOLUME OF RESERVOIR BUFFER (7. ...Details: 1.5 ML DROPS OF PROTEIN-INHIBITOR SOLUTION (5.0 MG/ML IN 10 MILLIMOLAR TRIS-HCL, PH 8.5, 10 MILLI-MOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) WERE MIXED WITH AN EQUAL VOLUME OF RESERVOIR BUFFER (7.2% PEG-6000 (W:W), 0.10 M PIPES PH 5.8, 10 MILLIMOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) AND INCUBATED AT ROOM TEMPERATURE. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Apr 9, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 8445 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 2.96 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.047 |
Reflection | *PLUS Highest resolution: 2.73 Å / % possible obs: 87 % / Num. measured all: 26257 |
Reflection shell | *PLUS Highest resolution: 2.73 Å / Lowest resolution: 2.83 Å |
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Processing
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: ICE INHIBITED BY ACE-YVAD-CHO Resolution: 2.73→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.73→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.73→2.83 Å / Rfactor Rfree error: 0.067 / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: ICE288.PAR / Topol file: ICE288.TOP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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