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Open data
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Basic information
Entry | Database: PDB / ID: 7b9m | ||||||
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Title | Cys-45-tethered stabilizer 3 of 14-3-3(sigma)/ERa PPI | ||||||
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![]() | SIGNALING PROTEIN / protein-protein interaction / stabilization / hub protein / transcription factor | ||||||
Function / homology | ![]() 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 / protein kinase C inhibitor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis ...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 / protein kinase C inhibitor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / positive regulation of epidermal cell differentiation / epithelial cell proliferation involved in mammary gland duct elongation / keratinocyte development / epithelial cell development / keratinization / prostate epithelial cord elongation / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / TFIIB-class transcription factor binding / Regulation of localization of FOXO transcription factors / androgen metabolic process / steroid hormone receptor signaling pathway / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / mammary gland alveolus development / 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 / nuclear receptor-mediated steroid hormone signaling pathway / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / RHO GTPases activate PKNs / protein localization to chromatin / 14-3-3 protein binding / protein kinase A signaling / protein sequestering activity / TBP-class protein binding / negative regulation of innate immune response / nitric-oxide synthase regulator activity / protein export from nucleus / steroid binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / negative regulation of miRNA transcription / positive regulation of nitric-oxide synthase activity / stem cell proliferation / cellular response to estradiol stimulus / transcription coregulator binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / stem cell differentiation / nuclear estrogen receptor binding / 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 / negative regulation of DNA-binding transcription factor activity / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / response to estrogen / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / ATPase binding / fibroblast proliferation / regulation of inflammatory response / 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sijbesma, E. / Ottmann, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Exploration of a 14-3-3 PPI Pocket by Covalent Fragments as Stabilizers. Authors: Sijbesma, E. / Hallenbeck, K.K. / Andrei, S.A. / Rust, R.R. / Adriaans, J.M.C. / 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 | ![]() | 74.2 KB | Display | ![]() |
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PDB format | ![]() | 52.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 385.8 KB | Display | ![]() |
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Full document | ![]() | 385.8 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 24 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7b9rC ![]() 7b9tC ![]() 7ba3C ![]() 7ba5C ![]() 7ba6C ![]() 7ba7C ![]() 7ba8C ![]() 7ba9C ![]() 7baaC ![]() 7babC ![]() 4jc3S 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
#1: Protein | Mass: 26569.939 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Protein/peptide | Mass: 870.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||||||
#3: Chemical | #4: Chemical | ChemComp-T4W / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.31 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 0.095 M HEPES, 0.19 M CaCl2, 27% (v/v) PEG400, 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: 1.5419 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 18, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→66.26 Å / Num. obs: 30939 / % possible obs: 95.9 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.026 / Rrim(I) all: 0.064 / Net I/σ(I): 22.1 / Num. measured all: 181967 / Scaling rejects: 8 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JC3 Resolution: 1.7→41.894 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.16 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.18 Å2 / Biso mean: 15.3591 Å2 / Biso min: 3.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→41.894 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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