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Yorodumi- PDB-4wn5: Crystal structure of the C-terminal Per-Arnt-Sim (PASb) of human ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wn5 | |||||||||||||||
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Title | Crystal structure of the C-terminal Per-Arnt-Sim (PASb) of human HIF-3alpha9 bound to 18:1-1-monoacylglycerol | |||||||||||||||
Components | Hypoxia-inducible factor 3-alpha | |||||||||||||||
Keywords | TRANSCRIPTION / HIF-3alpha / PAS domain / monoacylglycerol / lipid / fatty acid | |||||||||||||||
Function / homology | Function and homology information : / Transcriptional regulation of pluripotent stem cells / chromatin => GO:0000785 / Regulation of gene expression by Hypoxia-inducible Factor / post-translational protein modification / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Neddylation / angiogenesis / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific ...: / Transcriptional regulation of pluripotent stem cells / chromatin => GO:0000785 / Regulation of gene expression by Hypoxia-inducible Factor / post-translational protein modification / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Neddylation / angiogenesis / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / protein ubiquitination / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / apoptotic process / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | |||||||||||||||
Authors | Fala, A.M. / Oliveira, J.F. / Dias, S.M. / Ambrosio, A.L. | |||||||||||||||
Funding support | Brazil, 4items
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Citation | Journal: Sci Rep / Year: 2015 Title: Unsaturated fatty acids as high-affinity ligands of the C-terminal Per-ARNT-Sim domain from the Hypoxia-inducible factor 3 alpha. Authors: Fala, A.M. / Oliveira, J.F. / Adamoski, D. / Aricetti, J.A. / Dias, M.M. / Dias, M.V.B. / Sforca, M.L. / Lopes-de-Oliveira, P.S. / Rocco, S.A. / Caldana, C. / Dias, S.M.G. / Ambrosio, A.L.B. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wn5.cif.gz | 157.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wn5.ent.gz | 126.9 KB | Display | PDB format |
PDBx/mmJSON format | 4wn5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wn5_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 4wn5_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 4wn5_validation.xml.gz | 15 KB | Display | |
Data in CIF | 4wn5_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/4wn5 ftp://data.pdbj.org/pub/pdb/validation_reports/wn/4wn5 | HTTPS FTP |
-Related structure data
Related structure data | 4h6jS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12520.955 Da / Num. of mol.: 2 / Fragment: unp residues 235-345 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HIF3A, BHLHE17, MOP7, PASD7 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 / References: UniProt: Q9Y2N7 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-P6G / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.06 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 3% PEG 400, 1.95 M ammonium sulfate, 0.1 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97724 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 25, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97724 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→28.5 Å / Num. obs: 68827 / % possible obs: 99.6 % / Redundancy: 9.8 % / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.15→1.17 Å / Redundancy: 9.1 % / % possible all: 99.4 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4h6j Resolution: 1.15→28.5 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 10.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→28.5 Å
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Refine LS restraints |
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LS refinement shell |
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