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Yorodumi- PDB-6py8: Crystal structure of the RBPJ-NOTCH1-NRARP ternary complex bound ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6py8 | |||||||||
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Title | Crystal structure of the RBPJ-NOTCH1-NRARP ternary complex bound to DNA | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / NOTCH1 / NRARP / RBPJ / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information negative regulation of Notch signaling pathway involved in somitogenesis / regulation of reproductive process / regulation of generation of precursor metabolites and energy / blood vessel endothelial cell fate specification / positive regulation of ERBB signaling pathway / club cell differentiation / arterial endothelial cell fate commitment / blood vessel lumenization / somite rostral/caudal axis specification / regulation of timing of cell differentiation ...negative regulation of Notch signaling pathway involved in somitogenesis / regulation of reproductive process / regulation of generation of precursor metabolites and energy / blood vessel endothelial cell fate specification / positive regulation of ERBB signaling pathway / club cell differentiation / arterial endothelial cell fate commitment / blood vessel lumenization / somite rostral/caudal axis specification / regulation of timing of cell differentiation / positive regulation of ephrin receptor signaling pathway / secondary heart field specification / pulmonary valve development / positive regulation of cell proliferation involved in heart morphogenesis / Defective LFNG causes SCDO3 / dorsal aorta morphogenesis / 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 / sebaceous gland development / 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 T cell differentiation / 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 / 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 / aortic valve development / auditory receptor cell fate commitment / positive regulation of aorta morphogenesis / negative regulation of endothelial cell chemotaxis / atrioventricular node development / neuroendocrine cell differentiation / collecting duct development / negative regulation of extracellular matrix constituent secretion / positive regulation of transcription of Notch receptor target / 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 / regulation of extracellular matrix assembly / endocardial cell differentiation / 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 / cardiac left ventricle morphogenesis / epidermal cell fate specification / coronary vein morphogenesis / negative regulation of collagen biosynthetic process / cardiac vascular smooth muscle cell development / pituitary gland development / negative regulation of myotube differentiation / somatic stem cell division / left/right axis specification / NOTCH2 intracellular domain regulates transcription / negative regulation of cardiac muscle hypertrophy / negative regulation of cell adhesion molecule production / interleukin-17-mediated signaling pathway / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of endothelial cell differentiation / apoptotic process involved in embryonic digit morphogenesis / endocardium development / positive regulation of cardiac epithelial to mesenchymal transition / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / Pre-NOTCH Processing in Golgi / cardiac epithelial to mesenchymal transition / atrioventricular canal development / cellular response to follicle-stimulating hormone stimulus / pericardium morphogenesis / cardiac atrium morphogenesis / cardiac muscle cell myoblast differentiation / negative regulation of catalytic activity / hair follicle maturation / negative regulation of calcium ion-dependent exocytosis / neuronal stem cell population maintenance / tissue regeneration / regulation of stem cell proliferation / negative regulation of oligodendrocyte differentiation / positive regulation of astrocyte differentiation Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.75 Å | |||||||||
Authors | Jarrett, S.M. / Seegar, T.C.M. / Blacklow, S.C. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Sci.Signal. / Year: 2019 Title: Extension of the Notch intracellular domain ankyrin repeat stack by NRARP promotes feedback inhibition of Notch signaling. Authors: Jarrett, S.M. / Seegar, T.C.M. / Andrews, M. / Adelmant, G. / Marto, J.A. / Aster, J.C. / Blacklow, S.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6py8.cif.gz | 351.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6py8.ent.gz | 274.5 KB | Display | PDB format |
PDBx/mmJSON format | 6py8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6py8_validation.pdf.gz | 493 KB | Display | wwPDB validaton report |
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Full document | 6py8_full_validation.pdf.gz | 516.6 KB | Display | |
Data in XML | 6py8_validation.xml.gz | 55.5 KB | Display | |
Data in CIF | 6py8_validation.cif.gz | 74.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/6py8 ftp://data.pdbj.org/pub/pdb/validation_reports/py/6py8 | HTTPS FTP |
-Related structure data
Related structure data | 2f8xS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 12505.126 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NRARP / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z6K4 #2: DNA chain | Mass: 5002.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: DNA chain | Mass: 4793.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #4: Protein | Mass: 50027.090 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBPJ, IGKJRB, IGKJRB1, RBPJK, RBPSUH / Production host: Escherichia coli (E. coli) / References: UniProt: Q06330 #5: Protein | Mass: 40859.293 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NOTCH1, TAN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P46531 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 50 mM Hepes pH 6.8, 200 mM Sodium Fluoride, 18% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.754→48.46 Å / Num. obs: 26271 / % possible obs: 99.17 % / Redundancy: 4.4 % / CC1/2: 0.998 / Net I/σ(I): 7.39 |
Reflection shell | Resolution: 3.754→3.888 Å / Num. unique obs: 2504 / CC1/2: 0.689 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2F8X Resolution: 3.75→48.46 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 35.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.75→48.46 Å
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Refine LS restraints |
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LS refinement shell |
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