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Open data
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Basic information
Entry | Database: PDB / ID: 3hqu | ||||||
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Title | PHD2:Fe:UN9:partial HIF1-alpha substrate complex | ||||||
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![]() | 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 | ![]() 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 cyclic-nucleotide phosphodiesterase activity / negative regulation of mesenchymal cell apoptotic process / hemoglobin biosynthetic process / positive regulation of hormone biosynthetic process / mesenchymal cell apoptotic process / regulation protein catabolic process at postsynapse / positive regulation of mitophagy / retina vasculature development in camera-type eye / Cellular response to hypoxia / intestinal epithelial cell maturation / negative regulation of growth / regulation of protein neddylation / collagen metabolic process / PTK6 Expression / intracellular oxygen homeostasis / negative regulation of bone mineralization / B-1 B cell homeostasis / vascular endothelial growth factor production / labyrinthine layer development / cardiac muscle tissue morphogenesis / 2-oxoglutarate-dependent dioxygenase activity / transcription regulator activator activity / dopaminergic neuron differentiation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / heart trabecula formation / regulation of modification of postsynaptic structure / lactate metabolic process / STAT3 nuclear events downstream of ALK signaling / positive regulation of cytokine production involved in inflammatory response / negative regulation of thymocyte apoptotic process / L-ascorbic acid binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / motile cilium / positive regulation of signaling receptor activity / insulin secretion involved in cellular response to glucose stimulus / negative regulation of TOR signaling / response to iron ion / response to muscle activity / neural crest cell migration / Regulation of gene expression by Hypoxia-inducible Factor / regulation of glycolytic process / embryonic hemopoiesis / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / PTK6 promotes HIF1A stabilization / regulation of aerobic respiration / digestive tract morphogenesis / response to nitric oxide / muscle cell cellular homeostasis / ventricular septum morphogenesis / positive regulation of neuroblast proliferation / axonal transport of mitochondrion / positive regulation of epithelial cell migration / bone mineralization / heart looping / outflow tract morphogenesis / E-box binding / intracellular glucose homeostasis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of vascular endothelial growth factor production / TOR signaling / neuroblast proliferation / negative regulation of reactive oxygen species metabolic process / embryonic placenta development / positive regulation of blood vessel endothelial cell migration / epithelial to mesenchymal transition / cellular response to interleukin-1 / regulation of angiogenesis / cis-regulatory region sequence-specific DNA binding / chondrocyte differentiation / positive regulation of chemokine production / axon cytoplasm / positive regulation of endothelial cell proliferation / lactation / positive regulation of glycolytic process / negative regulation of miRNA transcription / positive regulation of erythrocyte differentiation / positive regulation of nitric-oxide synthase activity / response to reactive oxygen species / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / euchromatin / visual learning / ferrous iron binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chowdhury, R. / McDonough, M.A. / Schofield, C.J. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.4 KB | Display | ![]() |
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PDB format | ![]() | 45 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 728 KB | Display | ![]() |
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Full document | ![]() | 729.4 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hqrC ![]() 2g19S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27525.314 Da / Num. of mol.: 1 / Fragment: PHD2 catalytic domain, residues 181-426 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.) ![]() ![]() ![]() 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 (HYP564) / Source: (synth.) ![]() |
#3: Chemical | ChemComp-FE2 / |
#4: Chemical | ChemComp-UN9 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.24 % / Mosaicity: 0.34 ° |
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Crystal grow | Temperature: 298 K / Method: hanging drop / pH: 6.5 Details: 1.6M AMMONIUM SULFATE, 4% DIOXANE, 0.1M MES PH6.5, ARGON ATMOSPHERE, 20MG/ML PROTEIN WITH 1MM FE(II)SO4, 10MM HIF1A-CODD-OH PEPTIDE, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 8, 2005 Details: Rh coated collimating mirror, a double crystal Si(III) monochromator with horizontal saggital focusing system, and finally a second Rh coated mirror for vertical focusing. |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.29 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 12581 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.068 / Χ2: 0.998 / Net I/σ(I): 16.658 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1193 / Χ2: 0.962 / % possible all: 96.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2G19 Resolution: 2.3→30.55 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 195390 / 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: 58.515 Å2 / ksol: 0.363 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.08 Å2 / Biso mean: 33.683 Å2 / Biso min: 1.07 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→30.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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