+Open data
-Basic information
Entry | Database: PDB / ID: 1jxq | ||||||
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Title | Structure of cleaved, CARD domain deleted Caspase-9 | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information caspase-9 / caspase complex / Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / leukocyte apoptotic process / glial cell apoptotic process / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / Caspase activation via Dependence Receptors in the absence of ligand ...caspase-9 / caspase complex / Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / leukocyte apoptotic process / glial cell apoptotic process / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / Caspase activation via Dependence Receptors in the absence of ligand / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / cysteine-type endopeptidase activity involved in apoptotic process / fibroblast apoptotic process / AKT phosphorylates targets in the cytosol / epithelial cell apoptotic process / platelet formation / Constitutive Signaling by AKT1 E17K in Cancer / protein maturation / enzyme activator activity / signal transduction in response to DNA damage / cellular response to dexamethasone stimulus / intrinsic apoptotic signaling pathway / kidney development / response to ischemia / NOD1/2 Signaling Pathway / protein processing / SH3 domain binding / positive regulation of neuron apoptotic process / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / response to estradiol / peptidase activity / neuron apoptotic process / response to lipopolysaccharide / response to hypoxia / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / DNA damage response / protein kinase binding / protein-containing complex / mitochondrion / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Renatus, M. / Stennicke, H.R. / Scott, F.L. / Liddington, R.C. / Salvesen, G.S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Dimer formation drives the activation of the cell death protease caspase 9. Authors: Renatus, M. / Stennicke, H.R. / Scott, F.L. / Liddington, R.C. / Salvesen, G.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jxq.cif.gz | 199.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jxq.ent.gz | 156.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/1jxq ftp://data.pdbj.org/pub/pdb/validation_reports/jx/1jxq | HTTPS FTP |
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-Related structure data
Related structure data | 1cp3S S: Starting model for refinement |
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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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Unit cell |
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-Components
#1: Protein | Mass: 31433.684 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pet23b / Production host: Escherichia coli (E. coli) References: GenBank: 1336027, UniProt: P55211*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Protein/peptide | Mass: 529.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This peptide was chemically synthesized. #3: Water | ChemComp-HOH / | Sequence details | TO FACILIATE COMPARISON WITH OTHER CASPASES THE CASPASE-1 (INTERLEUKIN 1-BETA CONVERTING ENZYME ...TO FACILIATE COMPARISON | |
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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: 2.719 Å3/Da / Density % sol: 54 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Mes pH 6.5, 12% PEG 20,000, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: unknown | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 111 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 26, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 33394 / Num. obs: 33394 / % possible obs: 99.4 % / Redundancy: 3 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 3.9 / % possible all: 93.2 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. measured all: 112744 |
Reflection shell | *PLUS % possible obs: 93.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Caspase-3 PDB entry 1CP3 Resolution: 2.8→19.91 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: restraint / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 31.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→19.91 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: restraint | |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.96 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top | |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Num. reflection obs: 31628 / σ(F): 2 / Num. reflection Rfree: 1650 / % reflection Rfree: 4.9 % / Rfactor obs: 0.233 / Rfactor Rfree: 0.276 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 31.9 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.35 / % reflection Rfree: 5.4 % / Rfactor Rwork: 0.283 |