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Yorodumi- PDB-8bwz: fragment-linked stabilizer for ERa - 14-3-3 interaction (1074393) -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bwz | ||||||
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Title | fragment-linked stabilizer for ERa - 14-3-3 interaction (1074393) | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / 14-3-3 / ERa / fragment linking / stabilization | ||||||
Function / homology | Function and homology information regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / negative regulation of keratinocyte proliferation ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / negative regulation of keratinocyte proliferation / Activation of BAD and translocation to mitochondria / establishment of skin barrier / negative regulation of protein localization to plasma membrane / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / RHO GTPases activate PKNs / negative regulation of innate immune response / protein sequestering activity / protein kinase A signaling / protein export from nucleus / positive regulation of cell adhesion / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / 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 / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / regulation of protein localization / positive regulation of cell growth / regulation of cell cycle / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Visser, E.J. / Vandenboorn, E.M.F. / Ottmann, C. | ||||||
Funding support | Netherlands, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2023 Title: From Tethered to Freestanding Stabilizers of 14-3-3 Protein-Protein Interactions through Fragment Linking. Authors: Visser, E.J. / Jaishankar, P. / Sijbesma, E. / Pennings, M.A.M. / Vandenboorn, E.M.F. / Guillory, X. / Neitz, R.J. / Morrow, J. / Dutta, S. / Renslo, A.R. / Brunsveld, L. / Arkin, M.R. / Ottmann, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bwz.cif.gz | 112.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bwz.ent.gz | 85 KB | Display | PDB format |
PDBx/mmJSON format | 8bwz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bwz_validation.pdf.gz | 762 KB | Display | wwPDB validaton report |
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Full document | 8bwz_full_validation.pdf.gz | 763.6 KB | Display | |
Data in XML | 8bwz_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 8bwz_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/8bwz ftp://data.pdbj.org/pub/pdb/validation_reports/bw/8bwz | HTTPS FTP |
-Related structure data
Related structure data | 8bwjC 8bwxC 8bx0C 8bx3C 8bx4C 8bxiC 8bxmC 8bxnC 8bxoC 8bxqC 8bxsC 8by9C 8bybC 8bycC 8bydC 8byeC 8byfC 8bygC 8byoC 8byyC 8byzC 8bz0C 8bz9C 8bzaC 8bzbC 8bzwC 8c04C 8c0kC 8c4fC 8c4gC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26558.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947 |
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#2: Protein/peptide | Mass: 613.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#3: Chemical | ChemComp-S3I / ~{ |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.12 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.095 M HEPES (pH 7.3), PEG400 (25% (v/v)), 0.19 M CaCl2 and 5% (v/v) Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→66.3 Å / Num. obs: 38522 / % possible obs: 99.8 % / Redundancy: 12.4 % / CC1/2: 0.999 / Net I/σ(I): 27.6 |
Reflection shell | Resolution: 1.6→1.63 Å / Num. unique obs: 1898 / CC1/2: 0.985 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→45.51 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→45.51 Å
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Refine LS restraints |
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LS refinement shell |
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