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Yorodumi- PDB-2rr0: Structure of epidermal growth factor-like repeat 12 of mouse Notc... -
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-Basic information
Entry | Database: PDB / ID: 2rr0 | ||||||
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Title | Structure of epidermal growth factor-like repeat 12 of mouse Notch-1 receptor | ||||||
Components | Neurogenic locus notch homolog protein 1 | ||||||
Keywords | RECEPTOR / Notch / EGF-Like Domain / Activator / ANK repeat / Cell membrane / Developmental protein / Differentiation / Disulfide bond / Glycoprotein / Metal-binding / Notch signaling pathway / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Transmembrane | ||||||
Function / homology | Function and homology information 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 / 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 / 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 / epidermal cell fate specification / regulation of Notch signaling pathway / 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 / glial cell differentiation / positive regulation of cardiac epithelial to mesenchymal transition / cardiac epithelial to mesenchymal transition / negative regulation of calcium ion-dependent exocytosis / cardiac muscle cell myoblast differentiation / cellular response to follicle-stimulating hormone stimulus / neuron fate commitment / 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 Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Hosoguchi, K. / Shimizu, K. / Fujitani, N. / Nishimura, S. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: Chemical Synthesis, Folding, and Structural Insights into O-Fucosylated Epidermal Growth Factor-like Repeat 12 of Mouse Notch-1 Receptor Authors: Hiruma-Shimizu, K. / Hosoguchi, K. / Liu, Y. / Fujitani, N. / Ohta, T. / Hinou, H. / Matsushita, T. / Shimizu, H. / Feizi, T. / Nishimura, S. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rr0.cif.gz | 212.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rr0.ent.gz | 183.4 KB | Display | PDB format |
PDBx/mmJSON format | 2rr0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rr/2rr0 ftp://data.pdbj.org/pub/pdb/validation_reports/rr/2rr0 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 4218.697 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN EGF-LIKE repeat 12 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q01705 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using a combination NOE and D2O exchange experiment. |
-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0 / pH: 5.3 / Pressure: ambient / Temperature: 300 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz |
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-Processing
NMR software | Name: CNS / Version: 1.1 / Classification: refinement |
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Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 1 |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1 |