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- PDB-1toz: NMR structure of the human NOTCH-1 ligand binding region -

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Basic information

Entry
Database: PDB / ID: 1toz
TitleNMR structure of the human NOTCH-1 ligand binding region
ComponentsNeurogenic locus notch homolog protein 1
KeywordsSIGNALING 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 / venous endothelial cell differentiation / retinal cone 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 / venous endothelial cell differentiation / retinal cone cell differentiation / arterial endothelial cell differentiation / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / 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 / negative regulation of photoreceptor cell differentiation / : / regulation of somitogenesis / endocardium morphogenesis / foregut morphogenesis / distal tubule development / inhibition of neuroepithelial cell differentiation / MAML1-RBP-Jkappa- ICN1 complex / regulation of epithelial cell proliferation involved in prostate gland development / cardiac chamber formation / auditory receptor cell fate commitment / negative regulation of endothelial cell chemotaxis / atrioventricular node development / positive regulation of transcription of Notch receptor target / positive regulation of aorta morphogenesis / neuroendocrine cell differentiation / cellular response to tumor cell / negative regulation of extracellular matrix constituent secretion / collecting duct development / compartment pattern specification / positive regulation of apoptotic process involved in morphogenesis / vasculogenesis involved in coronary vascular morphogenesis / regulation of extracellular matrix assembly / endocardial cell differentiation / chemical synaptic transmission, postsynaptic / epithelial to mesenchymal transition involved in endocardial cushion formation / T-helper 17 type immune response / cardiac ventricle morphogenesis / positive regulation of smooth muscle cell differentiation / epidermal cell fate specification / mesenchymal cell development / coronary vein morphogenesis / cardiac left ventricle morphogenesis / cardiac vascular smooth muscle cell development / negative regulation of myotube differentiation / left/right axis specification / negative regulation of catalytic activity / glomerular mesangial cell development / somatic stem cell division / negative regulation of cell adhesion molecule production / apoptotic process involved in embryonic digit morphogenesis / endocardium development / positive regulation of endothelial cell differentiation / negative regulation of cardiac muscle hypertrophy / regulation of cell adhesion involved in heart morphogenesis / positive regulation of cardiac epithelial to mesenchymal transition / cardiac epithelial to mesenchymal transition / interleukin-17-mediated signaling pathway / pericardium morphogenesis / cardiac atrium morphogenesis / Pre-NOTCH Processing in Golgi / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / negative regulation of collagen biosynthetic process / cardiac muscle cell myoblast differentiation / neuronal stem cell population maintenance / cellular response to follicle-stimulating hormone stimulus / negative regulation of calcium ion-dependent exocytosis / positive regulation of astrocyte differentiation / negative regulation of oligodendrocyte differentiation / tissue regeneration / regulation of stem cell proliferation / luteolysis / calcium-ion regulated exocytosis / heart trabecula morphogenesis / prostate gland epithelium morphogenesis / pulmonary valve morphogenesis / endoderm development / coronary artery morphogenesis / negative regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion mediated by cadherin / negative regulation of myoblast differentiation / negative regulation of biomineral tissue development / ventricular trabecula myocardium morphogenesis / tube formation / positive regulation of BMP signaling pathway / transcription regulator activator activity / positive regulation of keratinocyte differentiation / negative regulation of stem cell differentiation / astrocyte differentiation / inflammatory response to antigenic stimulus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / cardiac muscle tissue morphogenesis / Notch binding
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 domain / LNR (Lin-12/Notch) repeat profile. / Notch domain / Domain found in Notch and Lin-12 / EGF-like, conserved site / Human growth factor-like EGF / : / Calcium-binding EGF domain / Laminin / Laminin / 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 repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Neurogenic locus notch homolog protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHambleton, 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
DepositionJun 15, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)12,6001
Polymers12,6001
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 600structures with the lowest energy
RepresentativeModel #9fewest violations

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Components

#1: Protein Neurogenic locus notch homolog protein 1 / Notch 1 / hN1 / Translocation-associated notch protein TAN-1


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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HMQC-J
NMR detailsText: Additional torsion angle restraints derived using TALOS. Calcium atoms incorporated during structure calculations, and restraints incorporated based on the crystal structure 1EDM as described.

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Sample preparation

DetailsContents: 0.5-1mM protein / Solvent system: 90% H2O, 10% D2O, 15mM CaCl2, 0.02% NaN3
Sample conditionsIonic strength: 15mM CaCl2 / pH: 6.1 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
GE OMEGAGEOMEGA6001
GE OMEGAGEOMEGA7502
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.0.6Guntert, P.structure solution
CYANA1.0.6Guntert, P.refinement
RefinementMethod: 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 representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 600 / Conformers submitted total number: 20

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