+Open data
-Basic information
Entry | Database: PDB / ID: 8bzb | ||||||
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Title | co-soak stabilizers for ERa - 14-3-3 interaction (884_AZ275) | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / 14-3-3 / ERa / fragment linking / stabilization | ||||||
Function / homology | Function and homology information regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / regulation of epidermal cell division / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / protein kinase C inhibitor activity ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / regulation of epidermal cell division / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / protein kinase C inhibitor activity / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / positive regulation of epidermal cell differentiation / epithelial cell development / keratinocyte development / keratinization / prostate epithelial cord elongation / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / androgen metabolic process / TFIIB-class transcription factor binding / steroid hormone mediated signaling pathway / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / establishment of skin barrier / cellular response to estrogen stimulus / estrogen response element binding / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / : / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / intracellular steroid hormone receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / RHO GTPases activate PKNs / protein localization to chromatin / protein kinase A signaling / TBP-class protein binding / steroid binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / protein export from nucleus / negative regulation of innate immune response / 14-3-3 protein binding / nitric-oxide synthase regulator activity / ESR-mediated signaling / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / transcription corepressor binding / positive regulation of protein export from nucleus / negative regulation of miRNA transcription / cellular response to estradiol stimulus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of nitric-oxide synthase activity / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / SUMOylation of intracellular receptors / euchromatin / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / transcription coactivator binding / negative regulation of DNA-binding transcription factor activity / beta-catenin binding / Nuclear Receptor transcription pathway / positive regulation of DNA-binding transcription factor activity / response to estrogen / male gonad development / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / positive regulation of nitric oxide biosynthetic process / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / sequence-specific double-stranded DNA binding / response to estradiol / PIP3 activates AKT signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / fibroblast proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / Extra-nuclear estrogen signaling Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Visser, E.J. / Sijbesma, E. / 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 | 8bzb.cif.gz | 113.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bzb.ent.gz | 85.1 KB | Display | PDB format |
PDBx/mmJSON format | 8bzb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/8bzb ftp://data.pdbj.org/pub/pdb/validation_reports/bz/8bzb | HTTPS FTP |
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-Related structure data
Related structure data | 8bwjC 8bwxC 8bwzC 8bx0C 8bx3C 8bx4C 8bxiC 8bxmC 8bxnC 8bxoC 8bxqC 8bxsC 8by9C 8bybC 8bycC 8bydC 8byeC 8byfC 8bygC 8byoC 8byyC 8byzC 8bz0C 8bz9C 8bzaC 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
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 26531.955 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) / References: UniProt: P03372 |
-Non-polymers , 4 types, 314 molecules
#3: Chemical | #4: Chemical | ChemComp-GEH / | #5: Chemical | ChemComp-SH9 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.095 M HEPES (pH 7.1), PEG400 (24% (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: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→66.21 Å / Num. obs: 31123 / % possible obs: 97 % / Redundancy: 5.8 % / CC1/2: 0.999 / Net I/σ(I): 28.7 |
Reflection shell | Resolution: 1.7→1.73 Å / Num. unique obs: 1174 / CC1/2: 0.967 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→40.95 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.02 / 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: 1.7→40.95 Å
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Refine LS restraints |
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LS refinement shell |
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