+Open data
-Basic information
Entry | Database: PDB / ID: 4j3y | ||||||
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Title | Crystal structure of XIAP-BIR2 domain | ||||||
Components | E3 ubiquitin-protein ligase XIAP | ||||||
Keywords | APOPTOSIS / IAP / XIAP / CASPASE / APOPTOSIS INHIBITOR | ||||||
Function / homology | Function and homology information endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / 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 / protein serine/threonine kinase binding / nucleotide-binding oligomerization domain containing 2 signaling pathway ...endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / 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 / protein serine/threonine kinase binding / nucleotide-binding oligomerization domain containing 2 signaling pathway / 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 / TNFR1-induced proapoptotic signaling / regulation of innate immune response / RIPK1-mediated regulated necrosis / cysteine-type endopeptidase inhibitor activity / protein K63-linked ubiquitination / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of type I interferon production / negative regulation of tumor necrosis factor-mediated signaling pathway / Regulation of PTEN localization / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of protein ubiquitination / Deactivation of the beta-catenin transactivating complex / Regulation of TNFR1 signaling / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Regulation of necroptotic cell death / Wnt signaling pathway / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / positive regulation of canonical Wnt signaling pathway / ubiquitin protein ligase activity / regulation of cell population proliferation / regulation of inflammatory response / neuron apoptotic process / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / regulation of cell cycle / defense response to bacterium / DNA damage response / negative regulation of apoptotic process / 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: 1.45 Å | ||||||
Authors | Lukacs, C.M. / Janson, C.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: The structure of XIAP BIR2: understanding the selectivity of the BIR domains. Authors: Lukacs, C. / Belunis, C. / Crowther, R. / Danho, W. / Gao, L. / Goggin, B. / Janson, C.A. / Li, S. / Remiszewski, S. / Schutt, A. / Thakur, M.K. / Singh, S.K. / Swaminathan, S. / Pandey, R. ...Authors: Lukacs, C. / Belunis, C. / Crowther, R. / Danho, W. / Gao, L. / Goggin, B. / Janson, C.A. / Li, S. / Remiszewski, S. / Schutt, A. / Thakur, M.K. / Singh, S.K. / Swaminathan, S. / Pandey, R. / Tyagi, R. / Gosu, R. / Kamath, A.V. / Kuglstatter, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j3y.cif.gz | 82.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j3y.ent.gz | 61.6 KB | Display | PDB format |
PDBx/mmJSON format | 4j3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/4j3y ftp://data.pdbj.org/pub/pdb/validation_reports/j3/4j3y | HTTPS FTP |
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-Related structure data
Related structure data | 4j44C 4j45C 4j46C 4j47C 4j48C 1i3oS S: Starting model for refinement C: citing same article (ref.) |
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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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Details | Dimer in crystal is not biologically relevant |
-Components
#1: Protein | Mass: 9936.131 Da / Num. of mol.: 2 / Fragment: XIAP-BIR2 RESIDUES 152-236 / Mutation: C202A, C213G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: API3, BIRC4, IAP3, U32974, XIAP / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2(DE3)PLYSS References: UniProt: P98170, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Chemical | #3: 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: 1.9 Å3/Da / Density % sol: 35.1 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.7-1.9 M ammonium sulfate, 125 mM bis-tris propane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.45→38 Å / Num. obs: 27428 / % possible obs: 99.9 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.8 / % possible all: 99.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1I3O Resolution: 1.45→37.81 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.001 / SU ML: 0.045 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.349 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→37.81 Å
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