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- PDB-8or5: Solution NMR structure of Notch1 TMD -

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Basic information

Entry
Database: PDB / ID: 8or5
TitleSolution NMR structure of Notch1 TMD
ComponentsNotch 1 extracellular truncation
KeywordsMEMBRANE 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 / 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 / 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 / negative regulation of cell proliferation involved in heart valve morphogenesis / regulation of somitogenesis / endocardium morphogenesis / foregut morphogenesis / regulation of cell adhesion involved in heart 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 / positive regulation of aorta morphogenesis / negative regulation of endothelial cell chemotaxis / atrioventricular node development / positive regulation of transcription of Notch receptor target / neuroendocrine cell differentiation / negative regulation of extracellular matrix constituent secretion / cellular response to tumor cell / 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 / T-helper 17 type immune response / endocardial cell differentiation / chemical synaptic transmission, postsynaptic / epithelial to mesenchymal transition involved in endocardial cushion formation / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / cardiac ventricle morphogenesis / positive regulation of smooth muscle cell differentiation / mesenchymal cell development / epidermal cell fate specification / glomerular mesangial cell development / negative regulation of myotube differentiation / coronary vein morphogenesis / cardiac left ventricle morphogenesis / cardiac vascular smooth muscle cell development / left/right axis specification / somatic stem cell division / negative regulation of cell adhesion molecule production / tissue regeneration / negative regulation of catalytic activity / interleukin-17-mediated signaling pathway / endocardium development / apoptotic process involved in embryonic digit morphogenesis / positive regulation of endothelial cell differentiation / positive regulation of cardiac epithelial to mesenchymal transition / Pre-NOTCH Processing in Golgi / cardiac epithelial to mesenchymal transition / negative regulation of collagen biosynthetic process / pericardium morphogenesis / cardiac atrium morphogenesis / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / negative regulation of cardiac muscle hypertrophy / cellular response to follicle-stimulating hormone stimulus / negative regulation of calcium ion-dependent exocytosis / cardiac muscle cell myoblast differentiation / neuronal stem cell population maintenance / calcium-ion regulated exocytosis / negative regulation of oligodendrocyte differentiation / positive regulation of astrocyte differentiation / pulmonary valve morphogenesis / heart trabecula morphogenesis / regulation of stem cell proliferation / coronary artery morphogenesis / luteolysis / prostate gland epithelium morphogenesis / negative regulation of biomineral tissue development / endoderm development / negative regulation of myoblast differentiation / negative regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion mediated by cadherin / ventricular trabecula myocardium morphogenesis / tube formation / positive regulation of BMP signaling pathway / astrocyte differentiation / positive regulation of keratinocyte differentiation / transcription regulator activator activity / negative regulation of stem cell differentiation / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / inflammatory response to antigenic stimulus / cardiac muscle tissue morphogenesis / positive regulation of Ras protein signal transduction
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 / 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
Similarity search - Domain/homology
Neurogenic locus notch homolog protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsGuschtschin-Schmidt, N. / Muhle-Goll, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2290 Germany
CitationJournal: 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
DepositionApr 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Notch 1 extracellular truncation


Theoretical massNumber of molelcules
Total (without water)3,3651
Polymers3,3651
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 400structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Notch 1 extracellular truncation / NEXT


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-13C HSQC
141isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 500 uM Notch1 WT TMD, trifluoroethanol/water 80/20
Label: Notch1 WT / Solvent system: trifluoroethanol/water 80/20
SampleConc.: 500 uM / Component: Notch1 WT TMD / Isotopic labeling: natural abundance
Sample conditionsIonic strength units: mM / Label: 1 / pH: 6.5 / Pressure: 1 bar / Temperature: 300 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIA2.3.2Linge, O'Donoghue and Nilgesstructure calculation
CcpNmr Analysis2.4.2Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, Laue ED.chemical shift assignment
CcpNmr Analysis2.4.2Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, Laue ED.peak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 40

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