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Yorodumi- PDB-2f8x: Crystal structure of activated Notch, CSL and MAML on HES-1 promo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f8x | ||||||
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Title | Crystal structure of activated Notch, CSL and MAML on HES-1 promoter DNA sequence | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / Notch / CSL / Mastermind / Hes-1 / ankyrin repeats / Rel-Homology region / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information 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 / regulation of timing of cell differentiation / regulation of reproductive process / atrioventricular node cell development / positive regulation of ephrin receptor signaling pathway ...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 / regulation of timing of cell differentiation / regulation of reproductive process / atrioventricular node cell development / positive regulation of ephrin receptor signaling pathway / secondary heart field specification / positive regulation of cell proliferation involved in heart morphogenesis / pulmonary valve development / 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 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 / aortic valve 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 / 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 / cardiac ventricle morphogenesis / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / positive regulation of smooth muscle cell differentiation / 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 / 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 / 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 / atrioventricular canal development / 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 / hair follicle maturation / neuronal stem cell population maintenance / tissue regeneration / regulation of stem cell proliferation / negative regulation of oligodendrocyte differentiation / myeloid dendritic cell differentiation / positive regulation of astrocyte differentiation / calcium-ion regulated exocytosis / pulmonary valve morphogenesis Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Nam, Y. / Sliz, P. / Blacklow, S.C. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2006 Title: Structural basis for cooperativity in recruitment of MAML coactivators to Notch transcription complexes. Authors: Nam, Y. / Sliz, P. / Song, L. / 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 | 2f8x.cif.gz | 172.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f8x.ent.gz | 129.8 KB | Display | PDB format |
PDBx/mmJSON format | 2f8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/2f8x ftp://data.pdbj.org/pub/pdb/validation_reports/f8/2f8x | HTTPS FTP |
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-Related structure data
Related structure data | 2f8ySC 1ttuS 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
-DNA chain , 2 types, 2 molecules XY
#1: DNA chain | Mass: 5628.679 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 5401.517 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 3 types, 3 molecules CKM
#3: Protein | Mass: 49294.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRSETa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q06330 |
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#4: Protein | Mass: 27885.004 Da / Num. of mol.: 1 Fragment: [Contains: Notch 1 extracellular truncation; Notch 1 intracellular domain] Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NOTCH1, TAN1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P46531 |
#5: Protein | Mass: 7532.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAML1, KIAA0200 / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q92585 |
-Non-polymers , 1 types, 10 molecules
#6: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: hanging drop / pH: 7.9 Details: 50mM HEPES, 6% PEG 3350, and 5% ethylene glycol, pH 7.9, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||
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Components of the solutions |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9796 Å |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 10, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→44.82 Å / Num. all: 79964 / Num. obs: 72848 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.084 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 3.25→3.45 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 11314 / Rsym value: 0.411 / % possible all: 89.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries: 1TTU and 2F8Y Resolution: 3.25→44.82 Å / Isotropic thermal model: group / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 38.828 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 89.29 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.25→44.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.25→3.45 Å / Rfactor Rfree error: 0.015
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Xplor file |
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