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- PDB-3d6m: Crystal structure of human caspase-1 with a naturally-occurring L... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3d6m | ||||||
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Title | Crystal structure of human caspase-1 with a naturally-occurring Lys319->Arg substitution in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK) | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / catalytic domain / naturally-occurring mutation / Apoptosis / Hydrolase / Protease / Thiol protease / Zymogen / 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 | ![]() ![]() ![]() | ||||||
![]() | Rosen-Wolff, A. / Roesler, J. / Romanowski, M.J. | ||||||
![]() | ![]() Title: Mutated, structurally altered caspase-1 with decreased enzymatic and increased RIP2-meditated inflammatory activity leads to a new type of periodic fever (ICE fever). Authors: Rosen-Wolff, A. / Romanowski, M.J. / Ritter, L. / Flecks, S. / Quoos, N. / Gramatt, J. / Petzold, C. / Nguyen, H.D. / Gahr, M. / Roesler, 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 | ![]() | 74.2 KB | Display | ![]() |
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PDB format | ![]() | 54.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.4 KB | Display | ![]() |
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Full document | ![]() | 445.5 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 21 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3d6fC ![]() 3d6hC ![]() 1sc3S C: citing same article ( S: Starting model for refinement |
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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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Details | Dimer of the p20/p10 dimer |
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Components
#1: Protein | Mass: 20001.033 Da / Num. of mol.: 1 / Fragment: CASP1 p20 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 10417.965 Da / Num. of mol.: 1 / Fragment: CASP1 p10 / Mutation: K319R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein/peptide | |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.34 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Crystals obtained by hanging-drop vapor diffusion at 4 C (277K) against a reservoir of 0.1 M PIPES pH 6.0, 75-175 mM (NH4)2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3, and 2 mM MgCl2. All ...Details: Crystals obtained by hanging-drop vapor diffusion at 4 C (277K) against a reservoir of 0.1 M PIPES pH 6.0, 75-175 mM (NH4)2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3, and 2 mM MgCl2. All crystals cryoprotected in mother liquors supplemented with 20% (v/v) glycerol for 30-90 sec and immersion in liquid nitrogen., VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 160 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 30, 2006 |
Radiation | Monochromator: Asymmetric curved crystal; crystal type S(220) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 31131 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.8→1.87 Å / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1SC3 Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.612 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.155 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.863 Å / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Origin x: 65.6028 Å / Origin y: 23.963 Å / Origin z: 40.738 Å
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Refinement TLS group |
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