+Open data
-Basic information
Entry | Database: PDB / ID: 1jd5 | ||||||
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Title | Crystal Structure of DIAP1-BIR2/GRIM | ||||||
Components |
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Keywords | Hydrolase/Peptide / APOPTOSIS / GRIM / IAP / CASPASE ACTIVATION / DROSOPHILA / Hydrolase-Peptide complex | ||||||
Function / homology | Function and homology information SMAC, XIAP-regulated apoptotic response / DS ligand bound to FT receptor / larval central nervous system remodeling / negative regulation of compound eye retinal cell programmed cell death / antennal morphogenesis / Deactivation of the beta-catenin transactivating complex / Regulation of necroptotic cell death / Regulation of PTEN localization / melanization defense response / sensory organ precursor cell division ...SMAC, XIAP-regulated apoptotic response / DS ligand bound to FT receptor / larval central nervous system remodeling / negative regulation of compound eye retinal cell programmed cell death / antennal morphogenesis / Deactivation of the beta-catenin transactivating complex / Regulation of necroptotic cell death / Regulation of PTEN localization / melanization defense response / sensory organ precursor cell division / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / Regulation of PTEN stability and activity / spermatid nucleus differentiation / positive regulation of Toll signaling pathway / border follicle cell migration / positive regulation of border follicle cell migration / chaeta development / programmed cell death involved in cell development / caspase binding / programmed cell death / negative regulation of JNK cascade / protein neddylation / ubiquitin conjugating enzyme binding / NEDD8 ligase activity / ubiquitin-like protein conjugating enzyme binding / cysteine-type endopeptidase inhibitor activity / ubiquitin-specific protease binding / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / protein K48-linked ubiquitination / protein autoubiquitination / positive regulation of protein ubiquitination / determination of adult lifespan / apoptotic signaling pathway / RING-type E3 ubiquitin transferase / Wnt signaling pathway / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / spermatogenesis / neuron apoptotic process / regulation of cell cycle / positive regulation of apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / apoptotic process / perinuclear region of cytoplasm / protein homodimerization activity / mitochondrion / zinc ion binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Wu, J.W. / Cocina, A.E. / Chai, J. / Hay, B.A. / Shi, Y. | ||||||
Citation | Journal: Mol.Cell / Year: 2001 Title: Structural analysis of a functional DIAP1 fragment bound to grim and hid peptides. Authors: Wu, J.W. / Cocina, A.E. / Chai, J. / Hay, B.A. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jd5.cif.gz | 35.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jd5.ent.gz | 23.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jd5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jd5_validation.pdf.gz | 372.6 KB | Display | wwPDB validaton report |
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Full document | 1jd5_full_validation.pdf.gz | 372.6 KB | Display | |
Data in XML | 1jd5_validation.xml.gz | 3.5 KB | Display | |
Data in CIF | 1jd5_validation.cif.gz | 4.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/1jd5 ftp://data.pdbj.org/pub/pdb/validation_reports/jd/1jd5 | HTTPS FTP |
-Related 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: 14078.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: DIAP1 / Plasmid: PGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q24306 |
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#2: Protein/peptide | Mass: 1108.243 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This peptide was chemically synthesized. The sequence is naturally found in Drosophila melanogaster (fruit fly). References: UniProt: Q24570 |
#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: 2.44 Å3/Da / Density % sol: 49.59 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: TRIS, AMMONIUM DIHROGEN PHOSPHATE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 5, 2001 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→99 Å / Num. all: 12677 / Num. obs: 12525 / % possible obs: 98.8 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2 / Redundancy: 19 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 75 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 12 % / Rmerge(I) obs: 0.16 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Rfactor Rfree error: 0.012
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / σ(F): 1 / Rfactor obs: 0.202 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.261 / Rfactor Rwork: 0.237 |