+Open data
-Basic information
Entry | Database: PDB / ID: 8or5 | ||||||
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Title | Solution NMR structure of Notch1 TMD | ||||||
Components | Notch 1 extracellular truncation | ||||||
Keywords | MEMBRANE PROTEIN / Notch1 / gamma secretase / transmembrane | ||||||
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 / 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 / regulation of extracellular matrix assembly / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / cardiac ventricle morphogenesis / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / positive regulation of smooth muscle cell differentiation / cardiac left ventricle morphogenesis / mesenchymal cell development / 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 / 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 / endocardium development / apoptotic process involved in embryonic digit morphogenesis / positive regulation of cardiac epithelial to mesenchymal transition / Pre-NOTCH Processing in Golgi / cardiac epithelial to mesenchymal transition / negative regulation of calcium ion-dependent exocytosis / cardiac muscle cell myoblast differentiation / cellular response to follicle-stimulating hormone stimulus / pericardium morphogenesis / cardiac atrium morphogenesis / negative regulation of catalytic activity / neuronal stem cell population maintenance / 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 / endoderm development / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / prostate gland epithelium morphogenesis / luteolysis / cardiac muscle tissue morphogenesis / ventricular trabecula myocardium morphogenesis / negative regulation of myoblast differentiation / negative regulation of cell migration involved in sprouting angiogenesis / transcription regulator activator activity / positive regulation of BMP signaling pathway / tube formation / negative regulation of stem cell differentiation / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of keratinocyte differentiation / astrocyte differentiation / inflammatory response to antigenic stimulus / positive regulation of Ras protein signal transduction / negative regulation of ossification Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Guschtschin-Schmidt, N. / Muhle-Goll, C. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2023 Title: Permissive Conformations of a Transmembrane Helix Allow Intramembrane Proteolysis by gamma-Secretase. Authors: Ortner, M. / Guschtschin-Schmidt, N. / Stelzer, W. / Muhle-Goll, C. / Langosch, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8or5.cif.gz | 430.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8or5.ent.gz | 368.3 KB | Display | PDB format |
PDBx/mmJSON format | 8or5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/8or5 ftp://data.pdbj.org/pub/pdb/validation_reports/or/8or5 | HTTPS FTP |
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-Related structure data
Related structure data | 8oryC 8orzC 8os0C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 3365.254 Da / Num. of mol.: 1 / Fragment: Notch1 transmembrane domain / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P46531 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 500 uM Notch1 WT TMD, trifluoroethanol/water 80/20 Label: Notch1 WT / Solvent system: trifluoroethanol/water 80/20 |
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Sample | Conc.: 500 uM / Component: Notch1 WT TMD / Isotopic labeling: natural abundance |
Sample conditions | Ionic strength units: mM / Label: 1 / pH: 6.5 / Pressure: 1 bar / Temperature: 300 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 400 / Conformers submitted total number: 40 |