+Open data
-Basic information
Entry | Database: PDB / ID: 2vj3 | ||||||
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Title | Human Notch-1 EGFs 11-13 | ||||||
Components | NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1 | ||||||
Keywords | TRANSCRIPTION / METAL-BINDING / TRANSMEMBRANE / DEVELOPMENTAL PROTEIN / NOTCH SIGNALING PATHWAY / DIFFERENTIATION / PHOSPHORYLATION / EGF-LIKE DOMAIN / TRANSCRIPTION REGULATION / RECEPTOR / ACTIVATOR / ANK REPEAT / SIGNALLING / POLYMORPHISM / GLYCOPROTEIN / EXTRACELLULAR / EGF / NOTCH / JAGGED / NUCLEUS / CALCIUM / 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 / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / epithelial to mesenchymal transition involved in endocardial cushion formation / regulation of extracellular matrix assembly / endocardial cell differentiation / cardiac ventricle morphogenesis / cardiac left ventricle morphogenesis / mesenchymal cell development / epidermal cell fate specification / negative regulation of collagen biosynthetic process / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / negative regulation of myotube differentiation / somatic stem cell division / left/right axis specification / negative regulation of cell adhesion molecule production / negative regulation of cardiac muscle hypertrophy / positive regulation of endothelial cell differentiation / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / interleukin-17-mediated signaling pathway / apoptotic process involved in embryonic digit morphogenesis / endocardium development / positive regulation of cardiac epithelial to mesenchymal transition / cardiac epithelial to mesenchymal transition / Pre-NOTCH Processing in Golgi / 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 / tissue regeneration / neuronal stem cell population maintenance / tube formation / positive regulation of astrocyte differentiation / negative regulation of oligodendrocyte differentiation / endoderm development / regulation of stem cell proliferation / pulmonary valve morphogenesis / calcium-ion regulated exocytosis / heart trabecula morphogenesis / negative regulation of biomineral tissue development / negative regulation of cell-cell adhesion mediated by cadherin / coronary artery morphogenesis / prostate gland epithelium morphogenesis / luteolysis / cardiac muscle tissue morphogenesis / negative regulation of myoblast differentiation / ventricular trabecula myocardium morphogenesis / negative regulation of cell migration involved in sprouting angiogenesis / transcription regulator activator activity / positive regulation of BMP signaling pathway / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / negative regulation of stem cell differentiation / positive regulation of keratinocyte differentiation / astrocyte differentiation / negative regulation of ossification / inflammatory response to antigenic stimulus / enzyme inhibitor activity Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Johnson, S. / Cordle, J. / Tay, J.Z. / Roversi, P. / Lea, S.M. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2008 Title: A Conserved Face of the Jagged/Serrate Dsl Domain is Involved in Notch Trans-Activation and Cis-Inhibition. Authors: Cordle, J. / Johnson, S. / Tay, J.Z. / Roversi, P. / Wilkin, M.B. / De Madrid, B.H. / Shimizu, H. / Jensen, S. / Whiteman, P. / Jin, B. / Redfield, C. / Baron, M. / Lea, S.M. / 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 | 2vj3.cif.gz | 40 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vj3.ent.gz | 25.4 KB | Display | PDB format |
PDBx/mmJSON format | 2vj3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/2vj3 ftp://data.pdbj.org/pub/pdb/validation_reports/vj/2vj3 | HTTPS FTP |
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-Related structure data
Related structure data | 2vj2C 1edmS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14857.604 Da / Num. of mol.: 1 / Fragment: EGFS 11-13, RESIDUES 411-526 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM554 / References: UniProt: P46531 | ||||||||
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#2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | M477I IS A PUBLISHED CONFLICT. THE DETAILS OF WHICH CAN BE FOUND IN HAMBLETON ET AL (2004) ...M477I IS A PUBLISHED CONFLICT. THE DETAILS OF WHICH CAN BE FOUND IN HAMBLETON ET AL (2004) STRUCTURE. 12:2173-83 | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 46 % / Description: NONE |
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Crystal grow | pH: 5.7 Details: 30% (W/V) PEG-5000-MME, 100MM SODIUM ACETATE, PH5.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.542 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 25, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→24.25 Å / Num. obs: 4321 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 52.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 2.57→2.71 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 5.3 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EDM Resolution: 2.6→95.4 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO Details: BUSTER-TNT-GELLY 2.1.1 E. BLANC, P. ROVERSI, C. VONRHEIN, C. FLENSBURG, S. M. LEA AND G.BRICOGNE
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 124 Å2 / ksol: 0.34 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→95.4 Å
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Refine LS restraints |
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