+Open data
-Basic information
Entry | Database: PDB / ID: 8dgm | ||||||
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Title | 14-3-3 epsilon bound to phosphorylated PEAK1 (pT1165) peptide | ||||||
Components |
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Keywords | SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information : / regulation of heart rate by hormone / regulation of potassium ion transmembrane transporter activity / positive regulation of hippo signaling / membrane repolarization during cardiac muscle cell action potential / cytoplasmic sequestering of protein / negative regulation of toll-like receptor signaling pathway / regulation of membrane repolarization / protein localization to endoplasmic reticulum / NADE modulates death signalling ...: / regulation of heart rate by hormone / regulation of potassium ion transmembrane transporter activity / positive regulation of hippo signaling / membrane repolarization during cardiac muscle cell action potential / cytoplasmic sequestering of protein / negative regulation of toll-like receptor signaling pathway / regulation of membrane repolarization / protein localization to endoplasmic reticulum / NADE modulates death signalling / RAB GEFs exchange GTP for GDP on RABs / focal adhesion assembly / Signaling by Hippo / regulation of focal adhesion assembly / negative regulation of calcium ion export across plasma membrane / cytoplasmic pattern recognition receptor signaling pathway / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of heart rate by cardiac conduction / protein localization to nucleus / phosphoserine residue binding / calcium channel regulator activity / Regulation of HSF1-mediated heat shock response / Activation of BAD and translocation to mitochondria / HSF1 activation / potassium channel regulator activity / protein targeting / calcium channel inhibitor activity / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / signaling adaptor activity / RHO GTPases activate PKNs / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / regulation of cytosolic calcium ion concentration / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / protein sequestering activity / substantia nigra development / AURKA Activation by TPX2 / substrate adhesion-dependent cell spreading / positive regulation of protein export from nucleus / Translocation of SLC2A4 (GLUT4) to the plasma membrane / mitochondrial membrane / hippocampus development / TP53 Regulates Metabolic Genes / phosphoprotein binding / neuron migration / non-membrane spanning protein tyrosine kinase activity / cerebral cortex development / histone deacetylase binding / Regulation of PLK1 Activity at G2/M Transition / MAPK cascade / protein localization / actin cytoskeleton / melanosome / cell migration / MHC class II protein complex binding / cellular response to heat / scaffold protein binding / protein phosphatase binding / transmembrane transporter binding / protein autophosphorylation / protein kinase activity / intracellular signal transduction / cadherin binding / protein heterodimerization activity / protein domain specific binding / protein phosphorylation / focal adhesion / ubiquitin protein ligase binding / enzyme binding / signal transduction / endoplasmic reticulum / RNA binding / extracellular exosome / identical protein binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å | ||||||
Authors | Roy, M.J. / Hardy, J.M. / Lucet, I.S. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural mapping of PEAK pseudokinase interactions identifies 14-3-3 as a molecular switch for PEAK3 signaling. Authors: Roy, M.J. / Surudoi, M.G. / Kropp, A. / Hou, J. / Dai, W. / Hardy, J.M. / Liang, L.Y. / Cotton, T.R. / Lechtenberg, B.C. / Dite, T.A. / Ma, X. / Daly, R.J. / Patel, O. / Lucet, I.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dgm.cif.gz | 112.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dgm.ent.gz | 71.1 KB | Display | PDB format |
PDBx/mmJSON format | 8dgm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/8dgm ftp://data.pdbj.org/pub/pdb/validation_reports/dg/8dgm | HTTPS FTP |
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-Related structure data
Related structure data | 8dgnC 8dgoC 8dgpC 2br9S S: Starting model for refinement 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
#1: Protein | Mass: 29454.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAE / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P62258 | ||
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#2: Protein/peptide | Mass: 2329.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H792 | ||
#3: Chemical | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.8 M ammonium sulfate, 0.1 M HEPES pH 7.5, 5% (v/v) MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Liquid nitrogen / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2020 | ||||||||||||||||||||||||
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 3.2→45.71 Å / Num. obs: 6156 / % possible obs: 99.8 % / Redundancy: 18.8 % / CC1/2: 1 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.106 / Net I/σ(I): 20.2 | ||||||||||||||||||||||||
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
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BR9 Resolution: 3.2→45.71 Å / SU ML: 0.4446 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.5633 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 102.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→45.71 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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