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Yorodumi- PDB-3d8c: Factor inhibiting HIF-1 alpha D201G mutant in complex with ZN(II)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d8c | ||||||
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Title | Factor inhibiting HIF-1 alpha D201G mutant in complex with ZN(II), alpha-ketoglutarate and HIF-1 alpha 19mer | ||||||
Components |
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Keywords | TRANSCRIPTION REGULATOR / OXIDOREDUCTASE / FIH / HIF / DSBH / OXYGENASE / TRANSCRIPTION / HYPOXIA / INHIBITOR 2-OXOGLUTARATE / ASPARAGINYL HYDROXYLASE / Dioxygenase / Iron / Metal-binding / Nucleus / Transcription regulation | ||||||
Function / homology | Function and homology information hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding / oxygen sensor activity ...hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding / oxygen sensor activity / Notch binding / negative regulation of Notch signaling pathway / NF-kappaB binding / positive regulation of myoblast differentiation / ferrous iron binding / transcription corepressor activity / perinuclear region of cytoplasm / protein homodimerization activity / zinc ion binding / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS WITH 1H2N / Resolution: 2.1 Å | ||||||
Authors | McDonough, M.A. / Chowdhury, R. / 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 | 3d8c.cif.gz | 92.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d8c.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 3d8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/3d8c ftp://data.pdbj.org/pub/pdb/validation_reports/d8/3d8c | HTTPS FTP |
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-Related structure data
Related structure data | 2ilmC 1h2nS 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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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 40270.246 Da / Num. of mol.: 1 / Mutation: D201G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HIF1AN, FIH1 / Plasmid: PET28A(+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9NWT6, peptide-aspartate beta-dioxygenase |
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#2: Protein/peptide | Mass: 2051.189 Da / Num. of mol.: 1 / Fragment: CTAD / Source method: obtained synthetically / Details: SYNTHETIC PEPTIDE FRAGMENT OF HIF-1 ALPHA |
-Non-polymers , 5 types, 228 molecules
#3: Chemical | ChemComp-ZN / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-AKG / | #6: Chemical | ChemComp-GOL / | #7: 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 | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.6M AMMONIUM SULPHATE, 6% PEG400, 0.1M HEPES PH7.5, 24MG/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: Diamond / Beamline: I04 / Wavelength: 0.9696 / Wavelength: 0.9696 Å | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2008 / Details: MIRRORS | |||||||||
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→50 Å / Num. all: 33971 / Num. obs: 33850 / % possible obs: 99.7 % / Redundancy: 13.9 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.0434 / Net I/σ(I): 23.18 | |||||||||
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 3.66 / Num. unique all: 3288 / Rsym value: 0.2569 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS WITH 1H2N Starting model: 1H2N Resolution: 2.1→38.65 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 139071.03 / 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 82.0785 Å2 / ksol: 0.355882 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→38.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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