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- PDB-6y18: Ternary complex of 14-3-3 sigma (C38N), Estrogen Related Receptor... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6y18 | |||||||||
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Title | Ternary complex of 14-3-3 sigma (C38N), Estrogen Related Receptor gamma (DBD) phosphopeptide, and disulfide PPI stabilizer 3 | |||||||||
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![]() | PEPTIDE BINDING PROTEIN / 14-3-3 / ERRy phosphopeptide / disulfide / stabilization | |||||||||
Function / homology | ![]() AF-2 domain binding / nuclear steroid receptor activity / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding ...AF-2 domain binding / nuclear steroid receptor activity / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / retinoic acid receptor signaling pathway / establishment of skin barrier / estrogen response element binding / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / nuclear receptor-mediated steroid hormone signaling pathway / 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 / steroid binding / 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 protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Nuclear Receptor transcription pathway / nuclear receptor activity / intrinsic apoptotic signaling pathway in response to DNA damage / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / positive regulation of cell growth / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / cadherin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / zinc ion binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Somsen, B.A. / Ottmann, C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Fluorescence Anisotropy-Based Tethering for Discovery of Protein-Protein Interaction Stabilizers. Authors: Sijbesma, E. / Somsen, B.A. / Miley, G.P. / Leijten-van de Gevel, I.A. / Brunsveld, L. / Arkin, M.R. / 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 | ![]() | 115.7 KB | Display | ![]() |
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PDB format | ![]() | 89 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 805.5 KB | Display | ![]() |
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Full document | ![]() | 806.8 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 23.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xxcC ![]() 6xy5C ![]() 6y1dC ![]() 6y3wC ![]() 6y58C ![]() 3p1nS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 26553.875 Da / Num. of mol.: 1 / Mutation: C38N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1217.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 4 types, 365 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/O68.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/O68.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MG / |
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#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-O68 / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.61 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.095 M HEPES (pH 7.3), 0.19 M CaCl2, 25% (v/v) PEG 400 and 5% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→66.29 Å / Num. obs: 71139 / % possible obs: 99.9 % / Redundancy: 12.6 % / CC1/2: 0.998 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.3→1.32 Å / Mean I/σ(I) obs: 3.4 / Num. unique obs: 3469 / CC1/2: 0.883 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3P1N Resolution: 1.3→55.983 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.99
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.49 Å2 / Biso mean: 15.9688 Å2 / Biso min: 6.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3→55.983 Å
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LS refinement shell |
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