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Yorodumi- PDB-6eih: The crystal structure of 14-3-3 epsilon in complex with the phosp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eih | |||||||||||||||
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Title | The crystal structure of 14-3-3 epsilon in complex with the phosphorylated NELFE peptide | |||||||||||||||
Components |
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Keywords | PROTEIN BINDING / 14-3-3 / NELF | |||||||||||||||
Function / homology | Function and homology information negative regulation of peptidyl-serine dephosphorylation / regulation of heart rate by hormone / regulation of potassium ion transmembrane transporter activity / negative regulation of calcium ion transmembrane transporter activity / membrane repolarization during cardiac muscle cell action potential / regulation of membrane repolarization / NADE modulates death signalling / RAB GEFs exchange GTP for GDP on RABs / Signaling by Hippo / negative regulation of calcium ion export across plasma membrane ...negative regulation of peptidyl-serine dephosphorylation / regulation of heart rate by hormone / regulation of potassium ion transmembrane transporter activity / negative regulation of calcium ion transmembrane transporter activity / membrane repolarization during cardiac muscle cell action potential / regulation of membrane repolarization / NADE modulates death signalling / RAB GEFs exchange GTP for GDP on RABs / Signaling by Hippo / negative regulation of calcium ion export across plasma membrane / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / cytoplasmic pattern recognition receptor signaling pathway / regulation of heart rate by cardiac conduction / protein localization to nucleus / calcium channel regulator activity / phosphoserine residue binding / Regulation of HSF1-mediated heat shock response / HSF1 activation / Activation of BAD and translocation to mitochondria / potassium channel regulator activity / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / signaling adaptor activity / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / 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 / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of cytosolic calcium ion concentration / regulation of mitotic cell cycle / substantia nigra development / protein sequestering activity / AURKA Activation by TPX2 / positive regulation of protein export from nucleus / Translocation of SLC2A4 (GLUT4) to the plasma membrane / hippocampus development / mitochondrial membrane / TP53 Regulates Metabolic Genes / phosphoprotein binding / neuron migration / cerebral cortex development / histone deacetylase binding / Regulation of PLK1 Activity at G2/M Transition / MAPK cascade / melanosome / MHC class II protein complex binding / cellular response to heat / scaffold protein binding / protein phosphatase binding / transmembrane transporter binding / intracellular signal transduction / cadherin binding / protein heterodimerization activity / protein domain specific binding / focal adhesion / ubiquitin protein ligase binding / enzyme binding / signal transduction / RNA binding / extracellular exosome / membrane / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å | |||||||||||||||
Authors | Akutsu, M. / Wagner, S.A. / Beli, P. | |||||||||||||||
Funding support | Germany, 4items
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Citation | Journal: Nat Commun / Year: 2018 Title: p38-MK2 signaling axis regulates RNA metabolism after UV-light-induced DNA damage. Authors: Borisova, M.E. / Voigt, A. / Tollenaere, M.A.X. / Sahu, S.K. / Juretschke, T. / Kreim, N. / Mailand, N. / Choudhary, C. / Bekker-Jensen, S. / Akutsu, M. / Wagner, S.A. / Beli, P. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eih.cif.gz | 55.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eih.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 6eih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/6eih ftp://data.pdbj.org/pub/pdb/validation_reports/ei/6eih | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26371.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAE / Production host: unidentified plasmid (others) / References: UniProt: P62258 |
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#2: Protein/peptide | Mass: 542.501 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others) |
#3: 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: 2.42 Å3/Da / Density % sol: 49.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 40% pentaerythritol propoxylate, 0.2M sodium thiocyanate, 0.1M HEPES, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→46 Å / Num. obs: 7463 / % possible obs: 100 % / Redundancy: 13.1 % / Net I/σ(I): 18.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→46 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.9 / SU B: 12.769 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.355 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.54 Å2 / Biso mean: 50.554 Å2 / Biso min: 31.29 Å2
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Refinement step | Cycle: final / Resolution: 2.7→46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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