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Yorodumi- PDB-6g6x: 14-3-3sigma in complex with a P129beta3P mutated YAP pS127 phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g6x | |||||||||
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Title | 14-3-3sigma in complex with a P129beta3P mutated YAP pS127 phosphopeptide | |||||||||
Components |
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Keywords | ONCOPROTEIN / beta amino acid hippo pathway YAP/TAZ | |||||||||
Function / homology | Function and homology information 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 / hippo signaling / tissue homeostasis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / Formation of axial mesoderm / negative regulation of stem cell differentiation / embryonic heart tube morphogenesis / female germ cell nucleus / proline-rich region binding / Signaling by Hippo / negative regulation of epithelial cell differentiation / organ growth / positive regulation of stem cell population maintenance / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / 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 / regulation of neurogenesis / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / canonical Wnt signaling pathway / 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 / cellular response to retinoic acid / negative regulation of stem cell proliferation / extrinsic apoptotic signaling pathway / Nuclear signaling by ERBB4 / RHO GTPases activate PKNs / keratinocyte differentiation / positive regulation of cardiac muscle cell proliferation / protein kinase A signaling / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / epithelial cell proliferation / stem cell proliferation / positive regulation of epithelial cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / response to progesterone / negative regulation of extrinsic apoptotic signaling pathway / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / wound healing / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / 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 / transcription cis-regulatory region binding / regulation of cell cycle / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / DNA damage response / chromatin binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.13 Å | |||||||||
Authors | Andrei, S.A. / Thijssen, V. / Brunsveld, L. / Ottmann, C. / Milroy, L.G. | |||||||||
Funding support | Netherlands, 2items
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Citation | Journal: Chem.Commun.(Camb.) / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g6x.cif.gz | 185.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g6x.ent.gz | 150.2 KB | Display | PDB format |
PDBx/mmJSON format | 6g6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g6x_validation.pdf.gz | 442.8 KB | Display | wwPDB validaton report |
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Full document | 6g6x_full_validation.pdf.gz | 444 KB | Display | |
Data in XML | 6g6x_validation.xml.gz | 16 KB | Display | |
Data in CIF | 6g6x_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/6g6x ftp://data.pdbj.org/pub/pdb/validation_reports/g6/6g6x | HTTPS FTP |
-Related structure data
Related structure data | 6g8iC 6g8jC 6g8kC 6g8lC 6g8pC 6g8qC 3mhrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947 | ||||
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#2: Protein/peptide | Mass: 1175.190 Da / Num. of mol.: 1 / Mutation: Proline 129 to beta3-proline / Source method: obtained synthetically / Details: EOE = beta3-proline / Source: (synth.) Homo sapiens (human) / References: UniProt: P46937 | ||||
#3: Chemical | ChemComp-CL / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.76 % |
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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: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 18, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.13→45.49 Å / Num. obs: 107708 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 10.45 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.025 / Rrim(I) all: 0.086 / Net I/σ(I): 14.1 / Num. measured all: 1208392 / Scaling rejects: 9132 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3mhr Resolution: 1.13→45.49 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 16.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.71 Å2 / Biso mean: 17.7075 Å2 / Biso min: 4.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.13→45.49 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19 / % reflection obs: 100 %
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