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- PDB-3p3n: Factor inhibiting HIF-1 Alpha in complex with Notch 1 fragment mo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3p3n | ||||||
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Title | Factor inhibiting HIF-1 Alpha in complex with Notch 1 fragment mouse notch (1930-1949) peptide | ||||||
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![]() | OXIDOREDUCTASE/TRANSCRIPTION / Double Stranded Beta-Helix / hydroxylase / Iron binding / 2-oxoglutarate binding / Hypoxia Inducible Factor binding / Ankyrin Repeat domain binding / OXIDOREDUCTASE-TRANSCRIPTION complex | ||||||
Function / homology | ![]() Pre-NOTCH Processing in Golgi / regulation of cardioblast proliferation / regulation of inner ear auditory receptor cell differentiation / positive regulation of ephrin receptor signaling pathway / positive regulation of glial cell differentiation / osteoblast fate commitment / venous blood vessel morphogenesis / Activated NOTCH1 Transmits Signal to the Nucleus / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis ...Pre-NOTCH Processing in Golgi / regulation of cardioblast proliferation / regulation of inner ear auditory receptor cell differentiation / positive regulation of ephrin receptor signaling pathway / positive regulation of glial cell differentiation / osteoblast fate commitment / venous blood vessel morphogenesis / Activated NOTCH1 Transmits Signal to the Nucleus / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis / cardiac right ventricle formation / growth involved in heart morphogenesis / Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation / cell differentiation in spinal cord / retinal cone cell differentiation / venous endothelial cell differentiation / arterial endothelial cell differentiation / cardiac chamber formation / epithelial cell fate commitment / negative regulation of pro-B cell differentiation / negative regulation of inner ear auditory receptor cell differentiation / mitral valve formation / cell migration involved in endocardial cushion formation / glomerular mesangial cell development / negative regulation of photoreceptor cell differentiation / negative regulation of cell proliferation involved in heart valve morphogenesis / regulation of somitogenesis / inhibition of neuroepithelial cell differentiation / endocardium morphogenesis / atrioventricular node development / foregut morphogenesis / regulation of cell adhesion involved in heart morphogenesis / distal tubule development / MAML1-RBP-Jkappa- ICN1 complex / regulation of epithelial cell proliferation involved in prostate gland development / auditory receptor cell fate commitment / positive regulation of aorta morphogenesis / negative regulation of endothelial cell chemotaxis / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / neuroendocrine cell differentiation / collecting duct development / negative regulation of extracellular matrix constituent secretion / positive regulation of transcription of Notch receptor target / hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / cellular response to tumor cell / positive regulation of apoptotic process involved in morphogenesis / Notch-HLH transcription pathway / compartment pattern specification / vasculogenesis involved in coronary vascular morphogenesis / T-helper 17 type immune response / endocardial cushion development / regulation of extracellular matrix assembly / peptidyl-histidine dioxygenase activity / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / cardiac ventricle morphogenesis / positive regulation of smooth muscle cell differentiation / cardiac left ventricle morphogenesis / mesenchymal cell development / peptidyl-aspartic acid 3-dioxygenase activity / regulation of Notch signaling pathway / epidermal cell fate specification / coronary vein morphogenesis / negative regulation of collagen biosynthetic process / cardiac vascular smooth muscle cell development / negative regulation of myotube differentiation / somatic stem cell division / left/right axis specification / negative regulation of cardiac muscle hypertrophy / Cellular response to hypoxia / negative regulation of cell adhesion molecule production / interleukin-17-mediated signaling pathway / positive regulation of endothelial cell differentiation / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / apoptotic process involved in embryonic digit morphogenesis / endocardium development / glial cell differentiation / positive regulation of cardiac epithelial to mesenchymal transition / cardiac epithelial to mesenchymal transition / cellular response to follicle-stimulating hormone stimulus / negative regulation of calcium ion-dependent exocytosis / neuron fate commitment / pericardium morphogenesis / cardiac atrium morphogenesis / cardiac muscle cell myoblast differentiation / negative regulation of catalytic activity / carboxylic acid binding / neuronal stem cell population maintenance / positive regulation of vasculogenesis / tissue regeneration / regulation of stem cell proliferation / negative regulation of oligodendrocyte differentiation / positive regulation of astrocyte differentiation / calcium-ion regulated exocytosis / pulmonary valve morphogenesis / heart trabecula morphogenesis / negative regulation of biomineral tissue development Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | McDonough, M.A. / Schofield, C.J. | ||||||
![]() | ![]() Title: Asparaginyl hydroxylation of the Notch ankyrin repeat domain by factor inhibiting hypoxia-inducible factor Authors: Coleman, M.L. / Mcdonough, M.A. / Hewitson, K.S. / Coles, C. / Mecinovic, J. / Edelmann, M. / Cook, K.M. / Cockman, M.E. / Lancaster, D.E. / Kessler, B.M. / Oldham, N.J. / Ratcliffe, P.J. / 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 | ![]() | 90.4 KB | Display | ![]() |
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PDB format | ![]() | 66.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.1 KB | Display | ![]() |
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Full document | ![]() | 467.5 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 25.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2qc9C ![]() 3p3pC ![]() 1h2nS 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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1 | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 40328.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9NWT6, peptide-aspartate beta-dioxygenase |
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#2: Protein/peptide | Mass: 2161.312 Da / Num. of mol.: 1 / Fragment: UNP residues 1930-1949 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Non-polymers , 5 types, 174 molecules ![](data/chem/img/FE2.gif)
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![](data/chem/img/AKG.gif)
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#3: Chemical | ChemComp-FE2 / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-AKG / | #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.6M AMMONIUM SULFATE, 4% PEG400, 0.1M HEPES PH7.5, NITROGEN ATMOSPHERE, 20MG/ML PROTEIN WITH 1MM FE(II), 2.0MM 2OG AND 10MM PEPTIDE , VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 2, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.4→37.3 Å / Num. obs: 20888 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 11.8 % / Biso Wilson estimate: 37.2 Å2 / Rsym value: 0.155 / Net I/σ(I): 14.78 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 3.33 / Rsym value: 0.8 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1H2N Resolution: 2.4→37.3 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 310707.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME U OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 75.8104 Å2 / ksol: 0.348475 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→37.3 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.49 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
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Xplor file |
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