+Open data
-Basic information
Entry | Database: PDB / ID: 4cue | ||||||
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Title | Human Notch1 EGF domains 11-13 mutant T466V | ||||||
Components | NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1 | ||||||
Keywords | TRANSCRIPTION / METAL-BINDING / TRANSMEMBRANE / DEVELOPMENTAL / PROTEIN / NOTCH SIGNALING PATHWAY / DIFFERENTIATION / PHOSPHORYLATION / EGF-LIKE DOMAIN / REGULATION / RECEPTOR / ACTIVATOR / ANK REPEAT / SIGNALLING / GLYCOPROTEIN / EXTRACELLULAR / EGF / JAGGED / NUCLEUS / MEMBRANE | ||||||
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 / positive regulation of smooth muscle cell differentiation / 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 / epithelial to mesenchymal transition involved in endocardial cushion formation / regulation of extracellular matrix assembly / endocardial cell differentiation / cardiac ventricle morphogenesis / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / 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 / tube formation / regulation of stem cell proliferation / endoderm development / 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 / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / prostate gland epithelium morphogenesis / luteolysis / ventricular trabecula myocardium morphogenesis / cardiac muscle tissue morphogenesis / negative regulation of myoblast differentiation / transcription regulator activator activity / negative regulation of cell migration involved in sprouting angiogenesis / positive regulation of BMP signaling pathway / negative regulation of stem cell differentiation / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of keratinocyte differentiation / astrocyte differentiation / negative regulation of ossification / inflammatory response to antigenic stimulus / positive regulation of Ras protein signal transduction Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Taylor, P. / Takeuchi, H. / Sheppard, D. / Chillakuri, C. / Lea, S.M. / Haltiwanger, R.S. / Handford, P.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Fringe-Mediated Extension of O-Linked Fucose in the Ligand-Binding Region of Notch1 Increases Binding to Mammalian Notch Ligands. Authors: Taylor, P. / Takeuchi, H. / Sheppard, D. / Chillakuri, C. / Lea, S.M. / Haltiwanger, R.S. / Handford, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cue.cif.gz | 38.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cue.ent.gz | 25.3 KB | Display | PDB format |
PDBx/mmJSON format | 4cue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/4cue ftp://data.pdbj.org/pub/pdb/validation_reports/cu/4cue | HTTPS FTP |
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-Related structure data
Related structure data | 4cudC 4cufC 4d0eC 4d0fC 2vj3S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14855.631 Da / Num. of mol.: 1 / Fragment: EGF 11-13, RESIDUES 411-526 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P46531 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.31 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9797 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 3→50.67 Å / Num. obs: 3174 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 88.01 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 3→3.35 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.8 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VJ3 Resolution: 3→50.67 Å / Cor.coef. Fo:Fc: 0.8088 / Cor.coef. Fo:Fc free: 0.8485 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.487
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Displacement parameters | Biso mean: 105.16 Å2
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Refine analyze | Luzzati coordinate error obs: 0.621 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→50.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.35 Å / Total num. of bins used: 5
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