+Open data
-Basic information
Entry | Database: PDB / ID: 3ieg | ||||||
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Title | Crystal Structure of P58(IPK) TPR Domain at 2.5 A | ||||||
Components | DnaJ homolog subfamily C member 3 | ||||||
Keywords | CHAPERONE / TPR motif / Endoplasmic reticulum / TPR repeat / Unfolded protein response | ||||||
Function / homology | Function and homology information positive regulation of translation initiation in response to endoplasmic reticulum stress / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / protein folding in endoplasmic reticulum / misfolded protein binding / cellular response to cold / protein kinase inhibitor activity / smooth endoplasmic reticulum / endoplasmic reticulum unfolded protein response ...positive regulation of translation initiation in response to endoplasmic reticulum stress / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / protein folding in endoplasmic reticulum / misfolded protein binding / cellular response to cold / protein kinase inhibitor activity / smooth endoplasmic reticulum / endoplasmic reticulum unfolded protein response / Neutrophil degranulation / response to endoplasmic reticulum stress / proteolysis involved in protein catabolic process / negative regulation of protein kinase activity / protein-folding chaperone binding / endoplasmic reticulum lumen / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å | ||||||
Authors | Tao, J. / Sha, B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Crystal Structure of P58(IPK) TPR Fragment Reveals the Mechanism for its Molecular Chaperone Activity in UPR. Authors: Tao, J. / Petrova, K. / Ron, D. / Sha, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ieg.cif.gz | 147 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ieg.ent.gz | 123.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ieg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/3ieg ftp://data.pdbj.org/pub/pdb/validation_reports/ie/3ieg | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 41384.875 Da / Num. of mol.: 2 / Fragment: UNP residues 35-393 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dnajc3, P58(IPK), P58ipk / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q91YW3 #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: 3.48 Å3/Da / Density % sol: 64.61 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15% PEG 5000 MME, 100 mM Hepes pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 32991 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.51→39.28 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.878 / SU B: 10.117 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.544 / ESU R Free: 0.326 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 43.637 Å2
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Refinement step | Cycle: LAST / Resolution: 2.51→39.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.51→2.574 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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