+Open data
-Basic information
Entry | Database: PDB / ID: 1nw9 | ||||||
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Title | STRUCTURE OF CASPASE-9 IN AN INHIBITORY COMPLEX WITH XIAP-BIR3 | ||||||
Components |
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Keywords | APOPTOSIS / caspase-9 / XIAP / caspase inhibition / caspase activation / dimerization | ||||||
Function / homology | Function and homology information caspase-9 / caspase complex / Formation of apoptosome / apoptosome / endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / regulation of BMP signaling pathway ...caspase-9 / caspase complex / Formation of apoptosome / apoptosome / endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / regulation of BMP signaling pathway / copper ion homeostasis / nucleotide-binding oligomerization domain containing 1 signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / leukocyte apoptotic process / glial cell apoptotic process / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / protein serine/threonine kinase binding / nucleotide-binding oligomerization domain containing 2 signaling pathway / Caspase activation via Dependence Receptors in the absence of ligand / SMAC, XIAP-regulated apoptotic response / 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 / TNFR1-induced proapoptotic signaling / fibroblast apoptotic process / AKT phosphorylates targets in the cytosol / epithelial cell apoptotic process / platelet formation / RIPK1-mediated regulated necrosis / cysteine-type endopeptidase inhibitor activity / regulation of innate immune response / Constitutive Signaling by AKT1 E17K in Cancer / protein K63-linked ubiquitination / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / protein maturation / enzyme activator activity / positive regulation of type I interferon production / negative regulation of tumor necrosis factor-mediated signaling pathway / signal transduction in response to DNA damage / Regulation of PTEN localization / cellular response to dexamethasone stimulus / intrinsic apoptotic signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of protein ubiquitination / kidney development / response to ischemia / Deactivation of the beta-catenin transactivating complex / Regulation of TNFR1 signaling / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / NOD1/2 Signaling Pathway / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Regulation of necroptotic cell death / protein processing / Wnt signaling pathway / SH3 domain binding / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / positive regulation of canonical Wnt signaling pathway / positive regulation of neuron apoptotic process / cellular response to UV / ubiquitin protein ligase activity / intrinsic apoptotic signaling pathway in response to DNA damage / response to estradiol / regulation of cell population proliferation / peptidase activity / regulation of inflammatory response / neuron apoptotic process / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / response to lipopolysaccharide / response to hypoxia / regulation of cell cycle / defense response to bacterium / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / DNA damage response / negative regulation of apoptotic process / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Shiozaki, E.N. / Chai, J. / Rigotti, D.J. / Riedl, S.J. / Li, P. / Srinivasula, S.M. / Alnemri, E.S. / Fairman, R. / Shi, Y. | ||||||
Citation | Journal: Mol.Cell / Year: 2003 Title: Mechanism of XIAP-Mediated Inhibition of Caspase-9 Authors: Shiozaki, E.N. / Chai, J. / Rigotti, D.J. / Riedl, S.J. / Li, P. / Srinivasula, S.M. / Alnemri, E.S. / Fairman, R. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nw9.cif.gz | 77.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nw9.ent.gz | 58.2 KB | Display | PDB format |
PDBx/mmJSON format | 1nw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/1nw9 ftp://data.pdbj.org/pub/pdb/validation_reports/nw/1nw9 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11327.616 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC4 OR API3 OR IAP3 OR XIAP / Production host: Escherichia coli (E. coli) / References: UniProt: P98170 |
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#2: Protein | Mass: 30473.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P55211 |
#3: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.6 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Tris, potassium phosphate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.1 Å |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Nov 28, 2002 / Details: mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→99 Å / Num. all: 23206 / Num. obs: 23136 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.3→2.38 Å / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 99 Å / Num. measured all: 415375 / Rmerge(I) obs: 0.071 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.525 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.23 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |