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- PDB-7or5: Ternary complex of 14-3-3 sigma, NotchpS1917 phosphopeptide, and WQ162 -
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Open data
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Basic information
Entry | Database: PDB / ID: 7or5 | ||||||
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Title | Ternary complex of 14-3-3 sigma, NotchpS1917 phosphopeptide, and WQ162 | ||||||
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![]() | SIGNALING PROTEIN / protein-peptide complex small-molecule | ||||||
Function / homology | ![]() morphogenesis of a branching structure / negative regulation of endothelial cell differentiation / Defective LFNG causes SCDO3 / Pre-NOTCH Processing in the Endoplasmic Reticulum / positive regulation of transcription of Notch receptor target / positive regulation of smooth muscle cell differentiation / negative regulation of cell adhesion molecule production / Pre-NOTCH Processing in Golgi / NOTCH4 Activation and Transmission of Signal to the Nucleus / negative regulation of cell-cell adhesion mediated by cadherin ...morphogenesis of a branching structure / negative regulation of endothelial cell differentiation / Defective LFNG causes SCDO3 / Pre-NOTCH Processing in the Endoplasmic Reticulum / positive regulation of transcription of Notch receptor target / positive regulation of smooth muscle cell differentiation / negative regulation of cell adhesion molecule production / Pre-NOTCH Processing in Golgi / NOTCH4 Activation and Transmission of Signal to the Nucleus / negative regulation of cell-cell adhesion mediated by cadherin / mammary gland development / cell fate determination / vasculature development / Notch binding / NOTCH4 Intracellular Domain Regulates Transcription / branching involved in blood vessel morphogenesis / regulation of epidermal cell division / Notch-HLH transcription pathway / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / negative regulation of cell differentiation / hemopoiesis / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / epithelial to mesenchymal transition / establishment of skin barrier / cis-regulatory region sequence-specific DNA binding / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / protein kinase A signaling / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / negative regulation of protein kinase activity / wound healing / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Pre-NOTCH Transcription and Translation / intrinsic apoptotic signaling pathway in response to DNA damage / signaling receptor activity / positive regulation of cell growth / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / regulation of cell cycle / cadherin binding / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Centorrino, F. / Wu, Q. / Ottmann, C. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: A crystallography-based study of fragment extensions into the 14-3-3 binding groove Authors: Centorrino, F. / Wu, Q. / Cossar, P. / Brunsveld, L. / Ottmann, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 136.8 KB | Display | ![]() |
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PDB format | ![]() | 86.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 787.7 KB | Display | ![]() |
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Full document | ![]() | 789 KB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7opwC ![]() 7oq7C ![]() 7oq8C ![]() 7oq9C ![]() 7oqaC ![]() 7oqgC ![]() 7oqjC ![]() 7oqsC ![]() 7oquC ![]() 7oqwC ![]() 7or3C ![]() 7or7C ![]() 7or8C ![]() 7orgC ![]() 7orhC ![]() 7orsC ![]() 7ortC ![]() 4jc3S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 28226.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1334.450 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-09W / ~{ |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.43 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.095 M Hepes pH7.7, 26%PEG 400, 0.19 M CaCl2, and 5 % Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→34.41 Å / Num. obs: 26726 / % possible obs: 98.9 % / Redundancy: 13.3 % / Biso Wilson estimate: 11.83 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.049 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 4 / Num. unique obs: 1303 / CC1/2: 0.955 / % possible all: 95.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4jc3 Resolution: 1.8→34.41 Å / SU ML: 0.1447 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.2092 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→34.41 Å
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Refine LS restraints |
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LS refinement shell |
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