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Yorodumi- PDB-3d9t: CIAP1-BIR3 in complex with N-terminal peptide from Caspase-9 (ATPFQE) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d9t | ||||||
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Title | CIAP1-BIR3 in complex with N-terminal peptide from Caspase-9 (ATPFQE) | ||||||
Components |
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Keywords | APOPTOSIS / zinc finger / Cytoplasm / Metal-binding / Polymorphism / Zinc / Zinc-finger / Alternative splicing / Hydrolase / Protease / Thiol protease / Zymogen | ||||||
Function / homology | Function and homology information caspase-9 / caspase complex / negative regulation of ripoptosome assembly involved in necroptotic process / regulation of cysteine-type endopeptidase activity / FBXO family protein binding / Formation of apoptosome / apoptosome / regulation of RIG-I signaling pathway / positive regulation of protein K48-linked ubiquitination / regulation of non-canonical NF-kappaB signal transduction ...caspase-9 / caspase complex / negative regulation of ripoptosome assembly involved in necroptotic process / regulation of cysteine-type endopeptidase activity / FBXO family protein binding / Formation of apoptosome / apoptosome / regulation of RIG-I signaling pathway / positive regulation of protein K48-linked ubiquitination / regulation of non-canonical NF-kappaB signal transduction / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of necroptotic process / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / positive regulation of protein K63-linked ubiquitination / leukocyte apoptotic process / CD40 receptor complex / XY body / glial cell apoptotic process / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / negative regulation of necroptotic process / 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 / positive regulation of protein monoubiquitination / regulation of reactive oxygen species metabolic process / TNFR1-induced proapoptotic signaling / fibroblast apoptotic process / AKT phosphorylates targets in the cytosol / epithelial cell apoptotic process / platelet formation / RIPK1-mediated regulated necrosis / regulation of toll-like receptor signaling pathway / regulation of innate immune response / Apoptotic cleavage of cellular proteins / regulation of cell differentiation / Constitutive Signaling by AKT1 E17K in Cancer / non-canonical NF-kappaB signal transduction / necroptotic process / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / protein maturation / enzyme activator activity / canonical NF-kappaB signal transduction / signal transduction in response to DNA damage / response to cAMP / tumor necrosis factor-mediated signaling pathway / cellular response to dexamethasone stimulus / TICAM1, RIP1-mediated IKK complex recruitment / intrinsic apoptotic signaling pathway / IKK complex recruitment mediated by RIP1 / placenta development / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / positive regulation of protein ubiquitination / kidney development / TNFR2 non-canonical NF-kB pathway / response to ischemia / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / NOD1/2 Signaling Pathway / cytoplasmic side of plasma membrane / Regulation of necroptotic cell death / protein processing / SH3 domain binding / protein polyubiquitination / ubiquitin-protein transferase activity / 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 / protein-folding chaperone binding / transferase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / neuron apoptotic process / response to ethanol / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / response to lipopolysaccharide / transcription coactivator activity / response to hypoxia / cell surface receptor signaling pathway / regulation of cell cycle / Ub-specific processing proteases / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / protein-containing complex / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Kulathila, R. / Price, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: The structure of the BIR3 domain of cIAP1 in complex with the N-terminal peptides of SMAC and caspase-9. Authors: Kulathila, R. / Vash, B. / Sage, D. / Cornell-Kennon, S. / Wright, K. / Koehn, J. / Stams, T. / Clark, K. / Price, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d9t.cif.gz | 60.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d9t.ent.gz | 43.5 KB | Display | PDB format |
PDBx/mmJSON format | 3d9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/3d9t ftp://data.pdbj.org/pub/pdb/validation_reports/d9/3d9t | HTTPS FTP |
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-Related structure data
Related structure data | 3d9uC 1nw9S C: citing same article (ref.) 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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Details | The biological assembly is the heterodimeric complex of CIAP1-BIR3 with N-terminal peptide from Caspase-9 (ATPFQE). |
-Components
#1: Protein | Mass: 11174.601 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC2, API1, IAP2, MIHB, RNF48 / Plasmid: pNAT40 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q13490 #2: Protein/peptide | Mass: 691.728 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: peptide synthesized based on N-terminal fragment of Caspase-9 (ATPFQE). References: UniProt: P55211, caspase-9 #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.67 Å3/Da / Density % sol: 53.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 3.1M NA FORMATE,10% GLYCEROL,1.5MM PEPTIDE, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→61.2 Å / Num. all: 41742 / Num. obs: 40966 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 35.4 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 5.5 / Num. unique all: 4030 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1NW9 Resolution: 1.5→35.04 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 407066.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.8947 Å2 / ksol: 0.403914 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→35.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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