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- PDB-6g8p: 14-3-3sigma in complex with a P129beta3P and L132beta3L mutated Y... -
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Basic information
Entry | Database: PDB / ID: 6g8p | |||||||||
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Title | 14-3-3sigma in complex with a P129beta3P and L132beta3L mutated YAP pS127 phosphopeptide | |||||||||
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![]() | ONCOPROTEIN / beta amino acid / hippo pathway / YAP/TAZ | |||||||||
Function / homology | ![]() enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / bud elongation involved in lung branching / polarized epithelial cell differentiation ...enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / bud elongation involved in lung branching / polarized epithelial cell differentiation / notochord development / negative regulation of cilium assembly / lung epithelial cell differentiation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / heart process / trophectodermal cell differentiation / paraxial mesoderm development / regulation of stem cell proliferation / tissue homeostasis / hippo signaling / EGR2 and SOX10-mediated initiation of Schwann cell myelination / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / negative regulation of stem cell differentiation / Formation of axial mesoderm / embryonic heart tube morphogenesis / female germ cell nucleus / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / proline-rich region binding / Signaling by Hippo / negative regulation of epithelial cell differentiation / organ growth / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / positive regulation of stem cell population maintenance / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / RUNX2 regulates osteoblast differentiation / Zygotic genome activation (ZGA) / somatic stem cell population maintenance / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / regulation of neurogenesis / Activation of BAD and translocation to mitochondria / canonical Wnt signaling pathway / negative regulation of keratinocyte proliferation / vasculogenesis / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / positive regulation of osteoblast differentiation / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / Nuclear signaling by ERBB4 / RHO GTPases activate PKNs / keratinocyte differentiation / positive regulation of cardiac muscle cell proliferation / protein sequestering activity / protein kinase A signaling / negative regulation of innate immune response / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of epithelial cell proliferation / positive regulation of protein export from nucleus / stem cell proliferation / epithelial cell proliferation / response to progesterone / Translocation of SLC2A4 (GLUT4) to the plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / TP53 Regulates Metabolic Genes / transcription coregulator activity / negative regulation of protein kinase activity / wound healing / cell morphogenesis / cellular response to gamma radiation / positive regulation of protein localization to nucleus / transcription corepressor activity / intrinsic apoptotic signaling pathway in response to DNA damage / cell-cell junction / protein localization / positive regulation of canonical Wnt signaling pathway / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / protein-containing complex assembly / DNA-binding transcription factor binding / transcription coactivator activity / regulation of cell cycle / transcription cis-regulatory region binding / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Andrei, S.A. / Thijssen, V. / Brunsveld, L. / Ottmann, C. / Milroy, L.G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A study on the effect of synthetic alpha-to-beta3-amino acid mutations on the binding of phosphopeptides to 14-3-3 proteins. Authors: Andrei, S.A. / Thijssen, V. / Brunsveld, L. / Ottmann, C. / Milroy, L.G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 173.6 KB | Display | ![]() |
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PDB format | ![]() | 138.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6g6xC ![]() 6g8iC ![]() 6g8jC ![]() 6g8kC ![]() 6g8lC ![]() 6g8qC ![]() 3mhrS C: citing same article ( S: Starting model for refinement |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 26542.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Protein/peptide | Mass: 1189.217 Da / Num. of mol.: 1 / Fragment: UNP residues 124-133 / Source method: obtained synthetically / Details: EOE and B3L are beta3-amino acid mutations / Source: (synth.) ![]() | ||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.12 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.095 M HEPES, pH 7.1, 29% PEG 400, 0.19 M CaCl2, 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 18, 2016 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.9→66.08 Å / Num. obs: 22902 / % possible obs: 99.7 % / Redundancy: 11.2 % / Biso Wilson estimate: 15.47 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.026 / Rrim(I) all: 0.089 / Net I/σ(I): 21.1 / Num. measured all: 257393 / Scaling rejects: 1018 | |||||||||||||||||||||||||||
Reflection shell | CC1/2: 0.983 / Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3mhr Resolution: 1.9→41.592 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.16
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.11 Å2 / Biso mean: 22.0283 Å2 / Biso min: 6.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→41.592 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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