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- PDB-2rr0: Structure of epidermal growth factor-like repeat 12 of mouse Notc... -

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Basic information

Entry
Database: PDB / ID: 2rr0
TitleStructure of epidermal growth factor-like repeat 12 of mouse Notch-1 receptor
ComponentsNeurogenic locus notch homolog protein 1
KeywordsRECEPTOR / 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 / cardiac right ventricle formation / regulation of inner ear auditory receptor cell differentiation / osteoblast fate commitment / negative regulation of inner ear auditory receptor cell differentiation / positive regulation of aorta morphogenesis / negative regulation of photoreceptor cell differentiation / apoptotic process involved in embryonic digit morphogenesis / venous blood vessel morphogenesis / regulation of somitogenesis ...Pre-NOTCH Processing in Golgi / cardiac right ventricle formation / regulation of inner ear auditory receptor cell differentiation / osteoblast fate commitment / negative regulation of inner ear auditory receptor cell differentiation / positive regulation of aorta morphogenesis / negative regulation of photoreceptor cell differentiation / apoptotic process involved in embryonic digit morphogenesis / venous blood vessel morphogenesis / regulation of somitogenesis / foregut morphogenesis / regulation of epithelial cell proliferation involved in prostate gland development / positive regulation of ephrin receptor signaling pathway / positive regulation of glial cell differentiation / auditory receptor cell fate commitment / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / compartment pattern specification / endocardial cushion development / somatic stem cell division / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis / growth involved in heart morphogenesis / regulation of cardioblast proliferation / mesenchymal cell development / cell differentiation in spinal cord / venous endothelial cell differentiation / arterial endothelial cell differentiation / collecting duct development / cell migration involved in endocardial cushion formation / negative regulation of pro-B cell differentiation / prostate gland epithelium morphogenesis / mitral valve formation / negative regulation of cell proliferation involved in heart morphogenesis / endocardium morphogenesis / distal tubule development / MAML1-RBP-Jkappa- ICN1 complex / cardiac chamber formation / cardiac atrium morphogenesis / endoderm development / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / pericardium morphogenesis / atrioventricular node development / cardiac ventricle morphogenesis / positive regulation of transcription of Notch receptor target / negative regulation of endothelial cell chemotaxis / glomerular mesangial cell development / CSL-Notch-Mastermind transcription factor complex / cellular response to tumor cell / Notch-HLH transcription pathway / positive regulation of smooth muscle cell differentiation / cardiac septum morphogenesis / vasculogenesis involved in coronary vascular morphogenesis / negative regulation of extracellular matrix constituent secretion / Activated NOTCH1 Transmits Signal to the Nucleus / regulation of extracellular matrix assembly / chemical synaptic transmission, postsynaptic / positive regulation of apoptotic process involved in morphogenesis / endocardial cell differentiation / left/right axis specification / epithelial to mesenchymal transition involved in endocardial cushion formation / positive regulation of endothelial cell differentiation / cardiac left ventricle morphogenesis / embryonic hindlimb morphogenesis / negative regulation of myotube differentiation / coronary vein morphogenesis / negative regulation of glial cell proliferation / cardiac vascular smooth muscle cell development / neuronal stem cell population maintenance / endocardium development / positive regulation of astrocyte differentiation / cardiac muscle cell myoblast differentiation / negative regulation of stem cell differentiation / negative regulation of cell adhesion molecule production / T-helper 17 type immune response / glial cell differentiation / tissue regeneration / negative regulation of calcium ion-dependent exocytosis / positive regulation of cardiac epithelial to mesenchymal transition / skeletal muscle cell differentiation / cardiac epithelial to mesenchymal transition / regulation of Notch signaling pathway / embryonic limb morphogenesis / neuron fate commitment / regulation of cell adhesion involved in heart morphogenesis / heart trabecula morphogenesis / negative regulation of oligodendrocyte differentiation / interleukin-17-mediated signaling pathway / negative regulation of catalytic activity / negative regulation of myoblast differentiation / cellular response to follicle-stimulating hormone stimulus / negative regulation of collagen biosynthetic process / neural tube development / negative regulation of cardiac muscle hypertrophy / luteolysis / pulmonary valve morphogenesis / tube formation / determination of left/right symmetry / cardiac muscle tissue morphogenesis / oligodendrocyte differentiation
Similarity search - Function
Neurogenic locus notch homolog protein 1 / Notch, C-terminal / Domain of unknown function / : / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein / NOD ...Neurogenic locus notch homolog protein 1 / Notch, C-terminal / Domain of unknown function / : / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein / NOD / NODP / Notch-like domain superfamily / LNR (Lin-12/Notch) repeat profile. / LNR domain / Notch domain / Domain found in Notch and Lin-12 / EGF-like, conserved site / Human growth factor-like EGF / : / Calcium-binding EGF domain / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Ankyrin repeat / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Neurogenic locus notch homolog protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsHosoguchi, K. / Shimizu, K. / Fujitani, N. / Nishimura, S.
CitationJournal: 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
DepositionFeb 26, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurogenic locus notch homolog protein 1


Theoretical massNumber of molelcules
Total (without water)4,2191
Polymers4,2191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Neurogenic locus notch homolog protein 1 / Notch 1 / Motch A / mT14 / p300


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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H NOESY
1312D 1H-1H TOCSY
1422D 1H-1H TOCSY
NMR detailsText: The structure was determined using a combination NOE and D2O exchange experiment.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.75mM NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1; 90% H2O/10% D2O90% H2O/10% D2O
20.75mM NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1; 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.75 mMNEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1-11
0.75 mMNEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1-22
Sample conditionsIonic strength: 0 / pH: 5.3 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR softwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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