[English] 日本語
Yorodumi- PDB-6g8k: 14-3-3sigma in complex with a S131beta3S mutated YAP pS127 phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g8k | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 14-3-3sigma in complex with a S131beta3S mutated YAP pS127 phosphopeptide | |||||||||
Components |
| |||||||||
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 / contact inhibition / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / bud elongation involved in lung branching ...enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / contact inhibition / 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 / tissue homeostasis / hippo signaling / regulation of stem cell proliferation / 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 / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of epithelial cell differentiation / negative regulation of fat cell differentiation / organ growth / positive regulation of stem cell population maintenance / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / RUNX2 regulates osteoblast differentiation / progesterone receptor signaling pathway / Zygotic genome activation (ZGA) / somatic stem cell population maintenance / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / regulation of neurogenesis / phosphoserine residue binding / canonical Wnt signaling pathway / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / positive regulation of osteoblast differentiation / vasculogenesis / Nuclear signaling by ERBB4 / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / RHO GTPases activate PKNs / keratinocyte differentiation / positive regulation of cardiac muscle cell proliferation / protein export from nucleus / negative regulation of innate immune response / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / response to progesterone / epithelial cell proliferation / stem cell proliferation / positive regulation of epithelial cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / cellular response to gamma radiation / wound healing / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / cell morphogenesis / positive regulation of protein localization to nucleus / positive regulation of canonical Wnt signaling pathway / transcription corepressor activity / intrinsic apoptotic signaling pathway in response to DNA damage / cell-cell junction / 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 / cell population proliferation / transcription coactivator activity / transcription cis-regulatory region binding / regulation of cell cycle / cadherin binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å | |||||||||
Authors | Andrei, S.A. / Thijssen, V. / Brunsveld, L. / Ottmann, C. / Milroy, L.G. | |||||||||
Funding support | Netherlands, 2items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6g8k.cif.gz | 176.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6g8k.ent.gz | 141.9 KB | Display | PDB format |
PDBx/mmJSON format | 6g8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/6g8k ftp://data.pdbj.org/pub/pdb/validation_reports/g8/6g8k | HTTPS FTP |
---|
-Related structure data
Related structure data | 6g6xC 6g8iC 6g8jC 6g8lC 6g8pC 6g8qC 3mhrS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein / Protein/peptide , 2 types, 2 molecules AP
#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 |
---|---|
#2: Protein/peptide | Mass: 1175.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: BSE is a beta3-serine unnatural amino acid / Source: (synth.) Homo sapiens (human) / References: UniProt: P46937*PLUS |
-Non-polymers , 4 types, 391 molecules
#3: Chemical | #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.53 % |
---|---|
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 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 8, 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: 1.25→66.24 Å / Num. obs: 79674 / % possible obs: 99.9 % / Redundancy: 11.7 % / Biso Wilson estimate: 12.32 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.03 / Rrim(I) all: 0.106 / Net I/σ(I): 12.4 / Num. measured all: 932846 / Scaling rejects: 435 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3mhr Resolution: 1.25→55.865 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.08
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.82 Å2 / Biso mean: 17.6523 Å2 / Biso min: 4.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.25→55.865 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
|