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Yorodumi- PDB-2iol: Crystal structure of the C-terminal MA3 domain of Pdcd4 (mouse); ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iol | ||||||
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Title | Crystal structure of the C-terminal MA3 domain of Pdcd4 (mouse); form 1 | ||||||
Components | Programmed Cell Death 4, Pdcd4 | ||||||
Keywords | ANTITUMOR PROTEIN / alpha-helical | ||||||
Function / homology | Function and homology information epithelial to mesenchymal transition involved in cardiac fibroblast development / negative regulation of myofibroblast differentiation / negative regulation of vascular associated smooth muscle cell differentiation / positive regulation of smooth muscle cell apoptotic process / negative regulation of JUN kinase activity / regulation of protein metabolic process / response to alkaloid / positive regulation of endothelial cell apoptotic process / positive regulation of vascular associated smooth muscle cell apoptotic process / negative regulation of vascular associated smooth muscle cell proliferation ...epithelial to mesenchymal transition involved in cardiac fibroblast development / negative regulation of myofibroblast differentiation / negative regulation of vascular associated smooth muscle cell differentiation / positive regulation of smooth muscle cell apoptotic process / negative regulation of JUN kinase activity / regulation of protein metabolic process / response to alkaloid / positive regulation of endothelial cell apoptotic process / positive regulation of vascular associated smooth muscle cell apoptotic process / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of cytokine production involved in inflammatory response / BMP signaling pathway / response to hormone / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / negative regulation of DNA-templated transcription / apoptotic process / negative regulation of apoptotic process / RNA binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Wlodawer, A. / LaRonde-LeBlanc, N.A. | ||||||
Citation | Journal: Mol.Cell.Biol. / Year: 2007 Title: Structural basis for inhibition of translation by the tumor suppressor pdcd4. Authors: Laronde-Leblanc, N. / Santhanam, A.N. / Baker, A.R. / Wlodawer, A. / Colburn, N.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iol.cif.gz | 59.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iol.ent.gz | 48.7 KB | Display | PDB format |
PDBx/mmJSON format | 2iol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/2iol ftp://data.pdbj.org/pub/pdb/validation_reports/io/2iol | HTTPS FTP |
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-Related 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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-Components
#1: Protein | Mass: 17506.424 Da / Num. of mol.: 2 / Fragment: C-terminal MA3 domain, residues 323-448 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pdcd4, TIS / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q61823 #2: 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: 3.33 Å3/Da / Density % sol: 63.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 1000, 0.1 M HEPES, 5% GLYCEROL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97174 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97174 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 27732 / Num. obs: 26640 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rsym value: 0.1 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.001→2.053 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.96 / Num. unique all: 1818 / Rsym value: 0.58 / % possible all: 95.93 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.903 / SU B: 11.115 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / ESU R: 0.185 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 51.668 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.001→2.053 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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