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Yorodumi- PDB-2ilm: Factor Inhibiting HIF-1 Alpha D201A Mutant in Complex with FE(II)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ilm | ||||||
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Title | Factor Inhibiting HIF-1 Alpha D201A Mutant in Complex with FE(II), Alpha-Ketoglutarate and HIF-1 Alpha 35mer | ||||||
Components | (Hypoxia-inducible factor 1 ...) x 2 | ||||||
Keywords | TRANSCRIPTION REGULATOR / OXIDOREDUCTASE / FIH / HIF / DSBH / OXYGENASE / TRANSCRIPTION / HYPOXIA / INHIBITOR 2-OXOGLUTARATE / ASPARAGINYL HYDROXYLASE | ||||||
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 / glandular epithelial cell maturation / elastin metabolic process / hypoxia-inducible factor-asparagine dioxygenase / : / regulation of transforming growth factor beta2 production ...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 / glandular epithelial cell maturation / elastin metabolic process / hypoxia-inducible factor-asparagine dioxygenase / : / regulation of transforming growth factor beta2 production / [protein]-asparagine 3-dioxygenase activity / connective tissue replacement involved in inflammatory response wound healing / peptidyl-histidine dioxygenase activity / cardiac ventricle morphogenesis / negative regulation of mesenchymal cell apoptotic process / hemoglobin biosynthetic process / peptidyl-aspartic acid 3-dioxygenase activity / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / positive regulation of hormone biosynthetic process / mesenchymal cell apoptotic process / retina vasculature development in camera-type eye / Cellular response to hypoxia / intestinal epithelial cell maturation / positive regulation of mitophagy / negative regulation of growth / regulation of protein neddylation / collagen metabolic process / PTK6 Expression / negative regulation of bone mineralization / intracellular oxygen homeostasis / carboxylic acid binding / B-1 B cell homeostasis / positive regulation of vasculogenesis / vascular endothelial growth factor production / ankyrin repeat binding / transcription regulator activator activity / E-box binding / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / dopaminergic neuron differentiation / 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 / motile cilium / positive regulation of vascular endothelial growth factor receptor signaling pathway / oxygen sensor activity / negative regulation of TOR signaling / positive regulation of signaling receptor activity / insulin secretion involved in cellular response to glucose stimulus / Notch binding / 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 / embryonic placenta development / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / regulation of aerobic respiration / muscle cell cellular homeostasis / positive regulation of neuroblast proliferation / negative regulation of Notch signaling pathway / positive regulation of epithelial cell migration / axonal transport of mitochondrion / bone mineralization / heart looping / outflow tract morphogenesis / intracellular glucose homeostasis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / NF-kappaB binding / cellular response to interleukin-1 / positive regulation of vascular endothelial growth factor production / neuroblast proliferation / negative regulation of reactive oxygen species metabolic process / TOR signaling / positive regulation of blood vessel endothelial cell migration / epithelial to mesenchymal transition / positive regulation of myoblast differentiation / cis-regulatory region sequence-specific DNA binding / chondrocyte differentiation / positive regulation of chemokine production / negative regulation of miRNA transcription / axon cytoplasm / positive regulation of endothelial cell proliferation / lactation / positive regulation of glycolytic process / positive regulation of erythrocyte differentiation / positive regulation of miRNA transcription / 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 / ferrous iron binding / visual learning / euchromatin / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / p53 binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS WITH 1H2N / Resolution: 2.3 Å | ||||||
Authors | Mcdonough, M.A. / Schofield, C.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Evidence that two enzyme-derived histidine ligands are sufficient for iron binding and catalysis by factor inhibiting HIF (FIH). Authors: Hewitson, K.S. / Holmes, S.L. / Ehrismann, D. / Hardy, A.P. / Chowdhury, R. / Schofield, C.J. / McDonough, M.A. #1: Journal: J.Biol.Chem. / Year: 2003 Title: Structure of Factor-Inhibiting Hypoxia-Inducible Factor (Hif) Reveals Mechanism of Oxidative Modification of Hif-1 Alpha Authors: Elkins, J.M. / Hewitson, K.S. / Mcneill, L.A. / Seibel, J.F. / Schlemminger, I. / Pugh, C.W. / Ratcliffe, P.J. / Schofield, C.J. #2: Journal: J.Am.Chem.Soc. / Year: 2005 Title: Selective inhibition of Factor Inhibiting Hypoxia inducible factor Authors: McDonough, M.A. / McNeill, L.A. / Tilliet, M. / Papamicael, C.A. / Chen, Q.Y. / Banerji, B. / Hewitson, K.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 | 2ilm.cif.gz | 90.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ilm.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ilm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ilm_validation.pdf.gz | 485.5 KB | Display | wwPDB validaton report |
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Full document | 2ilm_full_validation.pdf.gz | 492.7 KB | Display | |
Data in XML | 2ilm_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 2ilm_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/2ilm ftp://data.pdbj.org/pub/pdb/validation_reports/il/2ilm | HTTPS FTP |
-Related structure data
Related structure data | 3d8cC 1h2nS S: Starting model for refinement C: citing same article (ref.) |
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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
-Hypoxia-inducible factor 1 ... , 2 types, 2 molecules AS
#1: Protein | Mass: 40284.273 Da / Num. of mol.: 1 / Mutation: D201A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HIF1AN / Plasmid: PET28A(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9NWT6, peptide-aspartate beta-dioxygenase |
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#2: Protein/peptide | Mass: 4506.937 Da / Num. of mol.: 1 / Fragment: CTAD / Source method: obtained synthetically / Details: SYNTHETIC PEPTIDE FRAGMENT OF HIF-1 ALPHA / References: UniProt: Q16665 |
-Non-polymers , 6 types, 183 molecules
#3: Chemical | ChemComp-FE2 / | ||||||||
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#4: Chemical | #5: Chemical | ChemComp-BCT / | #6: Chemical | ChemComp-AKG / | #7: Chemical | #8: 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: 3.08 Å3/Da / Density % sol: 63 % Description: REJECTION CRITERIA AS REJECTION PROBABILITY, REJECTION |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.6M AMMONIUM SULPHATE, 6% PEG400, 0.1M HEPES PH7.5 ARGON ATMOSPHERE, 14MG/ML PROTEIN WITH 1MM FE(II)SO4, 1MM ALPHA-KETOGLUTARATE, 1MM HIF-1ALPHA PEPTIDE, VAPOR DIFFUSION, HANGING DROP, ...Details: 1.6M AMMONIUM SULPHATE, 6% PEG400, 0.1M HEPES PH7.5 ARGON ATMOSPHERE, 14MG/ML PROTEIN WITH 1MM FE(II)SO4, 1MM ALPHA-KETOGLUTARATE, 1MM HIF-1ALPHA PEPTIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 / Wavelength: 0.95372 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 21, 2004 / Details: BENT + TOROIDAL |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→43.27 Å / Num. obs: 25664 / % possible obs: 99.8 % / Redundancy: 11.4 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.029 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 11 % / Rmerge(I) obs: 0.4654 / Mean I/σ(I) obs: 2.18 / Rsym value: 0.3925 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS WITH 1H2N Starting model: 1H2N Resolution: 2.3→43.27 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 190630.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: BULK SOLVENT MODEL USED. The bicarbonate ion is a provisional assignment based on observed electron density. This molecule was not confirmed as being present in the crystallization solution.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 109.367 Å2 / ksol: 0.367653 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→43.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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