+Open data
-Basic information
Entry | Database: PDB / ID: 3hqr | ||||||
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Title | PHD2:Mn:NOG:HIF1-alpha substrate complex | ||||||
Components |
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Keywords | OXIDOREDUCTASE/TRANSCRIPTION / double stranded beta-helix / Alternative splicing / Congenital erythrocytosis / Dioxygenase / Disease mutation / Iron / Metal-binding / Oxidoreductase / Vitamin C / Zinc / Zinc-finger / Activator / Cytoplasm / DNA-binding / Hydroxylation / Isopeptide bond / Nucleus / Phosphoprotein / Polymorphism / S-nitrosylation / Transcription / Transcription regulation / Ubl conjugation / OXIDOREDUCTASE-TRANSCRIPTION COMPLEX | ||||||
Function / homology | Function and homology information epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / positive regulation of chemokine-mediated signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / elastin metabolic process / glandular epithelial cell maturation / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity ...epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / positive regulation of chemokine-mediated signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / elastin metabolic process / glandular epithelial cell maturation / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity / regulation of transforming growth factor beta2 production / peptidyl-proline dioxygenase activity / connective tissue replacement involved in inflammatory response wound healing / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / cardiac ventricle morphogenesis / negative regulation of mesenchymal cell apoptotic process / hemoglobin biosynthetic process / negative regulation of cyclic-nucleotide phosphodiesterase activity / retina vasculature development in camera-type eye / positive regulation of hormone biosynthetic process / regulation protein catabolic process at postsynapse / mesenchymal cell apoptotic process / collagen metabolic process / positive regulation of mitophagy / Cellular response to hypoxia / intestinal epithelial cell maturation / negative regulation of growth / regulation of protein neddylation / negative regulation of bone mineralization / PTK6 Expression / lactate metabolic process / intracellular oxygen homeostasis / B-1 B cell homeostasis / vascular endothelial growth factor production / labyrinthine layer development / 2-oxoglutarate-dependent dioxygenase activity / cardiac muscle tissue morphogenesis / negative regulation of TOR signaling / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / transcription regulator activator activity / dopaminergic neuron differentiation / STAT3 nuclear events downstream of ALK signaling / heart trabecula formation / regulation of modification of postsynaptic structure / positive regulation of cytokine production involved in inflammatory response / L-ascorbic acid binding / motile cilium / negative regulation of thymocyte apoptotic process / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of signaling receptor activity / insulin secretion involved in cellular response to glucose stimulus / response to iron ion / response to muscle activity / neural crest cell migration / embryonic hemopoiesis / Regulation of gene expression by Hypoxia-inducible Factor / regulation of glycolytic process / muscle cell cellular homeostasis / PTK6 promotes HIF1A stabilization / regulation of aerobic respiration / digestive tract morphogenesis / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / positive regulation of neuroblast proliferation / response to nitric oxide / ventricular septum morphogenesis / axonal transport of mitochondrion / positive regulation of epithelial cell migration / heart looping / bone mineralization / TOR signaling / E-box binding / outflow tract morphogenesis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / intracellular glucose homeostasis / neuroblast proliferation / positive regulation of vascular endothelial growth factor production / epithelial to mesenchymal transition / negative regulation of reactive oxygen species metabolic process / embryonic placenta development / positive regulation of blood vessel endothelial cell migration / cellular response to interleukin-1 / chondrocyte differentiation / regulation of angiogenesis / cis-regulatory region sequence-specific DNA binding / axon cytoplasm / positive regulation of chemokine production / lactation / positive regulation of endothelial cell proliferation / positive regulation of glycolytic process / response to reactive oxygen species / negative regulation of miRNA transcription / positive regulation of erythrocyte differentiation / positive regulation of nitric-oxide synthase activity / nuclear receptor binding / ferrous iron binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / euchromatin / visual learning Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Chowdhury, R. / McDonough, M.A. / Schofield, C.J. | ||||||
Citation | Journal: Structure / Year: 2009 Title: Structural basis for binding of hypoxia-inducible factor to the oxygen-sensing prolyl hydroxylases Authors: Chowdhury, R. / McDonough, M.A. / Mecinovic, J. / Loenarz, C. / Flashman, E. / Hewitson, K.S. / Domene, C. / Schofield, C.J. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2006 Title: Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2) Authors: McDonough, M.A. / Li, V. / Flashman, E. / Chowdhury, R. / Mohr, C. / Lienard, B.M.R. / Zondlo, J. / Oldham, N.J. / Clifton, I.J. / Lewis, J. / McNeill, L.A. / Kurzeja, R.J.M. / Hewitson, K.S. ...Authors: McDonough, M.A. / Li, V. / Flashman, E. / Chowdhury, R. / Mohr, C. / Lienard, B.M.R. / Zondlo, J. / Oldham, N.J. / Clifton, I.J. / Lewis, J. / McNeill, L.A. / Kurzeja, R.J.M. / Hewitson, K.S. / Yang, E. / Jordan, S. / Syed, R.S. / 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 | 3hqr.cif.gz | 69.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hqr.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 3hqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/3hqr ftp://data.pdbj.org/pub/pdb/validation_reports/hq/3hqr | HTTPS FTP |
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-Related structure data
Related structure data | 3hquC 2g19S C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 27439.199 Da / Num. of mol.: 1 / Fragment: PHD2 catalytic domain, residues 181-426 / Mutation: R398A Source method: isolated from a genetically manipulated source Details: HIS-tag cleaved with thrombin after Ni+ affinity purification followed by gel filtration Source: (gene. exp.) Homo sapiens (human) / Gene: PHD2 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9GZT9, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor |
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#2: Protein/peptide | Mass: 2026.287 Da / Num. of mol.: 1 / Fragment: C-terminal degradation domain, residues 558-574 / Source method: obtained synthetically / Details: peptide synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16665 |
#3: Chemical | ChemComp-MN / |
#4: Chemical | ChemComp-OGA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.660074 Å3/Da / Density % sol: 25.906935 % / Mosaicity: 1.147 ° |
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Crystal grow | Temperature: 298 K / Method: hanging drop / pH: 7.5 Details: 20% PEG 3350, 200mM MgCl2, pH 7.5, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 1, 2006 Details: Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 4.5 % / Av σ(I) over netI: 7.88 / Number: 69081 / Rmerge(I) obs: 0.157 / Χ2: 1.02 / D res high: 2 Å / D res low: 50 Å / Num. obs: 15231 / % possible obs: 99.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2→50 Å / Num. obs: 15231 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.157 / Χ2: 1.025 / Net I/σ(I): 7.879 / Num. measured all: 1658622 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 1.92 / Num. unique all: 1445 / Rsym value: 0.42 / Χ2: 0.801 / % possible all: 98 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2G19 Resolution: 2→34.18 Å / Rfactor Rfree error: 0.01 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 172620 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.2 Å2 / ksol: 0.372 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.51 Å2 / Biso mean: 25.254 Å2 / Biso min: 6.18 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→34.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.15 Å / Rfactor Rfree error: 0.063 / Total num. of bins used: 6
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Xplor file |
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