+Open data
-Basic information
Entry | Database: PDB / ID: 1toz | ||||||
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Title | NMR structure of the human NOTCH-1 ligand binding region | ||||||
Components | Neurogenic locus notch homolog protein 1 | ||||||
Keywords | SIGNALING PROTEIN / NOTCH / EGF / CALCIUM BINDING / LIGAND BINDING / MODULE | ||||||
Function / homology | Function and homology information Defective LFNG causes SCDO3 / 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 ...Defective LFNG causes SCDO3 / 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 / Pre-NOTCH Processing in the Endoplasmic Reticulum / 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 / neuroendocrine cell differentiation / collecting duct development / negative regulation of extracellular matrix constituent secretion / positive regulation of transcription of Notch receptor target / positive regulation of smooth muscle cell differentiation / cellular response to tumor cell / positive regulation of apoptotic process involved in morphogenesis / compartment pattern specification / vasculogenesis involved in coronary vascular morphogenesis / T-helper 17 type immune response / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / epithelial to mesenchymal transition involved in endocardial cushion formation / regulation of extracellular matrix assembly / endocardial cell differentiation / cardiac ventricle morphogenesis / mesenchymal cell development / cardiac left ventricle morphogenesis / epidermal cell fate specification / negative regulation of collagen biosynthetic process / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / negative regulation of myotube differentiation / somatic stem cell division / left/right axis specification / negative regulation of cell adhesion molecule production / negative regulation of cardiac muscle hypertrophy / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / positive regulation of endothelial cell differentiation / interleukin-17-mediated signaling pathway / apoptotic process involved in embryonic digit morphogenesis / endocardium development / positive regulation of cardiac epithelial to mesenchymal transition / cardiac epithelial to mesenchymal transition / Pre-NOTCH Processing in Golgi / cellular response to follicle-stimulating hormone stimulus / negative regulation of calcium ion-dependent exocytosis / cardiac muscle cell myoblast differentiation / pericardium morphogenesis / cardiac atrium morphogenesis / negative regulation of catalytic activity / tissue regeneration / neuronal stem cell population maintenance / tube formation / negative regulation of oligodendrocyte differentiation / positive regulation of astrocyte differentiation / endoderm development / regulation of stem cell proliferation / pulmonary valve morphogenesis / calcium-ion regulated exocytosis / heart trabecula morphogenesis / negative regulation of biomineral tissue development / negative regulation of cell-cell adhesion mediated by cadherin / coronary artery morphogenesis / prostate gland epithelium morphogenesis / luteolysis / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / cardiac muscle tissue morphogenesis / negative regulation of myoblast differentiation / ventricular trabecula myocardium morphogenesis / transcription regulator activator activity / negative regulation of cell migration involved in sprouting angiogenesis / positive regulation of BMP signaling pathway / negative regulation of stem cell differentiation / positive regulation of keratinocyte differentiation / astrocyte differentiation / negative regulation of ossification / inflammatory response to antigenic stimulus / enzyme inhibitor activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Hambleton, S. / Valeyev, N.Y. / Muranyi, A. / Knott, V. / Werner, J.M. / Mcmichael, A.J. / Handford, P.A. / Downing, A.K. | ||||||
Citation | Journal: STRUCTURE / Year: 2004 Title: Structural and functional properties of the human notch-1 ligand binding region Authors: Hambleton, S. / Valeyev, N.V. / Muranyi, A. / Knott, V. / Werner, J.M. / McMichael, A.J. / Handford, P.A. / Downing, A.K. #1: Journal: J.Biomol.Nmr / Year: 2004 Title: 1H, 13C, and 15N resonance assignments of human Notch-1 calcium binding EGF domains 11-13 Authors: Muranyi, A. / Hambleton, S. / Knott, V. / McMichael, A. / Handford, P.A. / Downing, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1toz.cif.gz | 643.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1toz.ent.gz | 556.3 KB | Display | PDB format |
PDBx/mmJSON format | 1toz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/1toz ftp://data.pdbj.org/pub/pdb/validation_reports/to/1toz | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 12600.011 Da / Num. of mol.: 1 / Fragment: NOTCH-1 EGF 11-13 / Mutation: M477I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pQE30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P46531 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: Additional torsion angle restraints derived using TALOS. Calcium atoms incorporated during structure calculations, and restraints incorporated based on the crystal structure 1EDM as described. |
-Sample preparation
Details | Contents: 0.5-1mM protein / Solvent system: 90% H2O, 10% D2O, 15mM CaCl2, 0.02% NaN3 |
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Sample conditions | Ionic strength: 15mM CaCl2 / pH: 6.1 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | ||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 Details: Input manually assigned 15N-edited NOESY peaks, unassigned 13C-edited NOESY peaks. See publication for further details. | ||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 600 / Conformers submitted total number: 20 |