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- PDB-8b4q: Ternary structure of 14-3-3s, ERRg phosphopeptide and dual-reacti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8b4q | ||||||
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Title | Ternary structure of 14-3-3s, ERRg phosphopeptide and dual-reactive compound 5 | ||||||
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![]() | PEPTIDE BINDING PROTEIN / 14-3-3 / hub-protein / dual-reactive compound | ||||||
Function / homology | ![]() AF-2 domain binding / nuclear steroid receptor activity / retinoic acid receptor signaling pathway / 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 ...AF-2 domain binding / nuclear steroid receptor activity / retinoic acid receptor signaling pathway / 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 / 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 sequestering activity / protein kinase A signaling / negative regulation of innate immune response / steroid binding / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / Nuclear Receptor transcription pathway / nuclear receptor activity / intrinsic apoptotic signaling pathway in response to DNA damage / sequence-specific double-stranded DNA binding / protein localization / 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 transcription by RNA polymerase II / chromatin / regulation of DNA-templated transcription / 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: Reversible Dual-Covalent Molecular Locking of the 14-3-3/ERR gamma Protein-Protein Interaction as a Molecular Glue Drug Discovery Approach. Authors: Somsen, B.A. / Schellekens, R.J.C. / Verhoef, C.J.A. / Arkin, M.R. / Ottmann, C. / Cossar, P.J. / Brunsveld, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.8 KB | Display | ![]() |
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PDB format | ![]() | 53.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8b2iC ![]() 8b2kC ![]() 8b5pC ![]() 8bfcC ![]() 8bi7C ![]() 8bjgC ![]() 8bjnC ![]() 8bm5C ![]() 6y1dS 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
-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 Details: GAMGS at the beginning (-5 to -1) are part of the expression tag Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1215.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 4 types, 340 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/OYI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/OYI.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-OYI / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.85 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.095 M Hepes pH 7.1, 0.19 M CaCl2, 25% PEG400, 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→45.55 Å / Num. obs: 56965 / % possible obs: 99.4 % / Redundancy: 13.4 % / CC1/2: 1 / Net I/σ(I): 34.7 |
Reflection shell | Resolution: 1.4→1.42 Å / Mean I/σ(I) obs: 9 / Num. unique obs: 33104 / CC1/2: 0.984 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6y1d Resolution: 1.4→45.55 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.9 Å2 / Biso mean: 15.0557 Å2 / Biso min: 5.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→45.55 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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