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Yorodumi- PDB-1h2k: Factor Inhibiting HIF-1 alpha in complex with HIF-1 alpha fragmen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h2k | ||||||
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Title | Factor Inhibiting HIF-1 alpha in complex with HIF-1 alpha fragment peptide | ||||||
Components |
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Keywords | TRANSCRIPTION ACTIVATOR/INHIBITOR / TRANSCRIPTION ACTIVATOR-INHIBITOR COMPLEX / FIH / HIF / DSBH / OXYGENASE / TRANSCRIPTION / HYPOXIA / 2- OXOGLUTARATE / ASPARAGINYL HYDROXYLASE / PHOSPHORYLATION | ||||||
Function / homology | Function and homology information epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / elastin metabolic process / hypoxia-inducible factor-1alpha signaling pathway / glandular epithelial cell maturation / positive regulation of chemokine-mediated signaling pathway / 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 / elastin metabolic process / hypoxia-inducible factor-1alpha signaling pathway / glandular epithelial cell maturation / positive regulation of chemokine-mediated signaling pathway / hypoxia-inducible factor-asparagine dioxygenase / : / regulation of transforming growth factor beta2 production / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / connective tissue replacement involved in inflammatory response wound healing / cardiac ventricle morphogenesis / negative regulation of mesenchymal cell apoptotic process / hemoglobin biosynthetic process / peptidyl-aspartic acid 3-dioxygenase activity / positive regulation of hormone biosynthetic process / retina vasculature development in camera-type eye / intestinal epithelial cell maturation / Cellular response to hypoxia / mesenchymal cell apoptotic process / negative regulation of growth / positive regulation of mitophagy / regulation of protein neddylation / PTK6 Expression / negative regulation of bone mineralization / collagen metabolic process / intracellular oxygen homeostasis / carboxylic acid binding / B-1 B cell homeostasis / positive regulation of vasculogenesis / vascular endothelial growth factor production / ankyrin repeat binding / dopaminergic neuron differentiation / lactate metabolic process / transcription regulator activator activity / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / 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 / response to muscle activity / negative regulation of TOR signaling / insulin secretion involved in cellular response to glucose stimulus / positive regulation of signaling receptor activity / embryonic hemopoiesis / oxygen sensor activity / Notch binding / response to iron ion / neural crest cell migration / regulation of glycolytic process / Regulation of gene expression by Hypoxia-inducible Factor / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / 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 / bone mineralization / axonal transport of mitochondrion / heart looping / intracellular glucose homeostasis / E-box binding / outflow tract morphogenesis / 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 / positive regulation of myoblast differentiation / positive regulation of blood vessel endothelial cell migration / TOR signaling / embryonic placenta development / epithelial to mesenchymal transition / chondrocyte differentiation / cis-regulatory region sequence-specific DNA binding / positive regulation of chemokine production / axon cytoplasm / positive regulation of endothelial cell proliferation / lactation / positive regulation of glycolytic process / positive regulation of erythrocyte differentiation / negative 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 / visual learning / ferrous iron binding / euchromatin / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cellular response to virus / cerebral cortex development Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å | ||||||
Authors | Elkins, J.M. / Hewitson, K.S. / McNeill, L.A. / Schlemminger, I. / Seibel, J.F. / Schofield, C.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Structure of Factor-Inhibiting Hypoxia-Inducible Factor (Hif) Reveals Mechanism of Oxidative Modification of Hif-1Alpha Authors: Elkins, J.M. / Hewitson, K.S. / McNeill, L.A. / Seibel, J.F. / Schlemminger, I. / Pugh, C. / Ratcliffe, P. / Schofield, C.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h2k.cif.gz | 89.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h2k.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 1h2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h2k_validation.pdf.gz | 462.8 KB | Display | wwPDB validaton report |
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Full document | 1h2k_full_validation.pdf.gz | 466.4 KB | Display | |
Data in XML | 1h2k_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 1h2k_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/1h2k ftp://data.pdbj.org/pub/pdb/validation_reports/h2/1h2k | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THE PROTEIN IS A DIMERIC FORMED BY CHAIN A.A HETERODIMERIC ASSOCIATION OF CHAIN A WITH CHAIN SPRODUCES A TETRAMER.THE BURIED SURFACE AREA SHOWN BELOW IS AN AVERAGECALCULATED FOR THE HETEROTETRAMER AND DOES NOTCORRESPOND TO THE BURIED SURFACE AREA FOR THEHOMODIMER OF CHAIN A |
-Components
-Protein / Protein/peptide , 2 types, 2 molecules AS
#1: Protein | Mass: 40328.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A(+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q969Q7, UniProt: Q9NWT6*PLUS |
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#2: Protein/peptide | Mass: 4506.937 Da / Num. of mol.: 1 Fragment: C-TERMINAL TRANSACTIVATION DOMAIN FRAGMENT, RESIDUES 786-826 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-GP-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q16665 |
-Non-polymers , 4 types, 198 molecules
#3: Chemical | ChemComp-FE2 / | ||
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#4: Chemical | ChemComp-OGA / | ||
#5: Chemical | #6: 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: 3.4 Å3/Da / Density % sol: 63 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 1.2M AMMONIUM SULPHATE, 4% PEG400, 0.1M HEPES PH7.5, ARGON ATMOSPHERE, 11MG/ML PROTEIN WITH 1MM FE(II), 2.5MM NOG AND 2.5MM PEPTIDE, pH 7.50 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→18.17 Å / Num. obs: 30574 / % possible obs: 99.2 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 1.5 / % possible all: 96 |
-Processing
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Refinement | Method to determine structure: MAD / Resolution: 2.15→18.5 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.588 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.73 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→18.5 Å
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