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Yorodumi- PDB-8q6d: Anaerobic crystal structure of HIF prolyl hydroxylase 2 (PHD2 181... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q6d | |||||||||||||||
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Title | Anaerobic crystal structure of HIF prolyl hydroxylase 2 (PHD2 181-407) in complex with HIF2alpha-CODD peptide (523-542), Fe(II) and 2-oxoglutarate (2OG) | |||||||||||||||
Components |
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Keywords | OXIDOREDUCTASE / 2OG oxygenases / oxygen sensor / jelly-roll | |||||||||||||||
Function / homology | Function and homology information myoblast fate commitment / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity / peptidyl-proline dioxygenase activity / negative regulation of cyclic-nucleotide phosphodiesterase activity / regulation protein catabolic process at postsynapse / Cellular response to hypoxia / regulation of protein neddylation / Transcriptional regulation of pluripotent stem cells ...myoblast fate commitment / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity / peptidyl-proline dioxygenase activity / negative regulation of cyclic-nucleotide phosphodiesterase activity / regulation protein catabolic process at postsynapse / Cellular response to hypoxia / regulation of protein neddylation / Transcriptional regulation of pluripotent stem cells / PTK6 Expression / intracellular oxygen homeostasis / labyrinthine layer development / norepinephrine metabolic process / 2-oxoglutarate-dependent dioxygenase activity / cardiac muscle tissue morphogenesis / heart trabecula formation / regulation of modification of postsynaptic structure / surfactant homeostasis / L-ascorbic acid binding / epithelial cell maturation / Regulation of gene expression by Hypoxia-inducible Factor / embryonic placenta development / response to nitric oxide / ventricular septum morphogenesis / blood vessel remodeling / regulation of angiogenesis / visual perception / Pexophagy / regulation of heart rate / erythrocyte differentiation / lung development / mitochondrion organization / mRNA transcription by RNA polymerase II / RNA polymerase II transcription regulatory region sequence-specific DNA binding / ferrous iron binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / multicellular organismal-level iron ion homeostasis / cellular response to hypoxia / Neddylation / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / angiogenesis / intracellular iron ion homeostasis / RNA polymerase II-specific DNA-binding transcription factor binding / response to oxidative stress / postsynaptic density / DNA-binding transcription factor activity, RNA polymerase II-specific / response to hypoxia / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / intracellular membrane-bounded organelle / glutamatergic synapse / regulation of transcription by RNA polymerase II / chromatin / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||||||||
Authors | Fiorini, G. / Figg Jr, W.D. / Schofield, C.J. | |||||||||||||||
Funding support | United Kingdom, 4items
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Citation | Journal: To Be Published Title: HIF prolyl hydroxylase 2 in complex with HIF2alpha-CODD Authors: Fiorini, G. / Figg Jr, W.D. / Schofield, C.J. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q6d.cif.gz | 155.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q6d.ent.gz | 122 KB | Display | PDB format |
PDBx/mmJSON format | 8q6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/8q6d ftp://data.pdbj.org/pub/pdb/validation_reports/q6/8q6d | HTTPS FTP |
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-Related structure data
Related structure data | 8q5sC 8q64C 8q6eC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26036.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EGLN1, C1orf12, PNAS-118, PNAS-137 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q9GZT9, hypoxia-inducible factor-proline dioxygenase |
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#2: Protein/peptide | Mass: 2309.544 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99814 |
#3: Chemical | ChemComp-FE / |
#4: Chemical | ChemComp-AKG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 34 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 10-35% PEG 4K, 0.2 ammonium acetate, sodium ammonium acetate trihydrate pH (4.1-5.6) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2021 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→38.07 Å / Num. obs: 42651 / % possible obs: 99.4 % / Redundancy: 12.6 % / CC1/2: 1 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.4→1.42 Å / Num. unique obs: 1834 / CC1/2: 0.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→36.55 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.58 / 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: 1.4→36.55 Å
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Refine LS restraints |
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LS refinement shell |
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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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