+Open data
-Basic information
Entry | Database: PDB / ID: 1xb0 | ||||||
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Title | Structure of the BIR domain of IAP-like protein 2 | ||||||
Components |
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Keywords | APOPTOSIS / SMAC / DIABLO / CASPASE INHIBITION / XIAP | ||||||
Function / homology | Function and homology information activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / CD40 receptor complex / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / intrinsic apoptotic signaling pathway in response to oxidative stress / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors ...activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / CD40 receptor complex / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / intrinsic apoptotic signaling pathway in response to oxidative stress / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway / positive regulation of protein ubiquitination / mitochondrial intermembrane space / cytoplasmic side of plasma membrane / positive regulation of canonical Wnt signaling pathway / activation of cysteine-type endopeptidase activity involved in apoptotic process / ubiquitin protein ligase activity / neuron apoptotic process / regulation of cell cycle / positive regulation of apoptotic process / apoptotic process / negative regulation of apoptotic process / mitochondrion / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Shin, H. / Renatus, M. / Eckelman, B.P. / Nunes, V.A. / Sampaio, C.A.M. / Salvesen, G.S. | ||||||
Citation | Journal: Biochem.J. / Year: 2005 Title: The BIR domain of IAP-like protein 2 is conformationally unstable: implications for caspase inhibition Authors: Shin, H. / Renatus, M. / Eckelman, B.P. / Nunes, V.A. / Sampaio, C.A.M. / Salvesen, G.S. | ||||||
History |
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Remark 999 | SEQUENCE Residues 253-261, of chains A-F, comprise an N-terminal fusion from A-F human XIAP |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xb0.cif.gz | 144.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xb0.ent.gz | 112.7 KB | Display | PDB format |
PDBx/mmJSON format | 1xb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/1xb0 ftp://data.pdbj.org/pub/pdb/validation_reports/xb/1xb0 | HTTPS FTP |
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-Related structure data
Related structure data | 1xb1C 1g73S 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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Unit cell |
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-Components
#1: Protein | Mass: 12349.910 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: XILP2: human ILP2 with an N-terminal fusion (residues 253-261 from human XIAP) Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC8, ILP2 / Plasmid: pet15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q96P09 #2: Protein/peptide | Mass: 726.883 Da / Num. of mol.: 6 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human). References: UniProt: Q9NR28 #3: Chemical | ChemComp-ZN / #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: 2.7 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 5% PEG3000, 100mM sodium acetate, 100mM Zinc acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.984 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 44152 / % possible obs: 98.2 % / Redundancy: 5.9 % / Rsym value: 0.074 |
Reflection shell | Resolution: 2.2→2.27 Å / Rsym value: 0.382 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1G73 (chain D) Resolution: 2.2→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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