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Yorodumi- PDB-2wh0: Recognition of an intrachain tandem 14-3-3 binding site within pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wh0 | ||||||
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Title | Recognition of an intrachain tandem 14-3-3 binding site within protein kinase C epsilon | ||||||
Components |
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Keywords | SIGNALING PROTEIN / TANDEM BINDING / PHOSPHOPROTEIN / 14-3-3 / CYTOPLASM / ACETYLATION / PKC EPSILON | ||||||
Function / homology | Function and homology information positive regulation of cellular glucuronidation / ethanol binding / TRAM-dependent toll-like receptor 4 signaling pathway / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / Golgi reassembly / DAG and IP3 signaling / positive regulation of lipid catabolic process / protein kinase C / negative regulation of sodium ion transmembrane transporter activity / mucus secretion ...positive regulation of cellular glucuronidation / ethanol binding / TRAM-dependent toll-like receptor 4 signaling pathway / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / Golgi reassembly / DAG and IP3 signaling / positive regulation of lipid catabolic process / protein kinase C / negative regulation of sodium ion transmembrane transporter activity / mucus secretion / diacylglycerol-dependent serine/threonine kinase activity / Effects of PIP2 hydrolysis / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / regulation of insulin secretion involved in cellular response to glucose stimulus / establishment of Golgi localization / macrophage activation involved in immune response / regulation of release of sequestered calcium ion into cytosol / response to morphine / Rap1 signalling / signaling receptor activator activity / cellular response to ethanol / synaptic transmission, GABAergic / positive regulation of fibroblast migration / positive regulation of cell-substrate adhesion / negative regulation of protein localization to nucleus / insulin secretion / intermediate filament cytoskeleton / positive regulation of mucus secretion / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / locomotory exploration behavior / positive regulation of wound healing / positive regulation of actin filament polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / positive regulation of epithelial cell migration / cell-substrate adhesion / positive regulation of cytokinesis / Regulation of localization of FOXO transcription factors / actin monomer binding / enzyme activator activity / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / Role of phospholipids in phagocytosis / cellular response to glucose starvation / 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 / regulation of peptidyl-tyrosine phosphorylation / RHO GTPases activate PKNs / negative regulation of protein ubiquitination / lipopolysaccharide-mediated signaling pathway / negative regulation of TORC1 signaling / negative regulation of innate immune response / SHC1 events in ERBB2 signaling / protein sequestering activity / regulation of ERK1 and ERK2 cascade / 14-3-3 protein binding / cell periphery / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / establishment of localization in cell / positive regulation of synaptic transmission, GABAergic / TP53 Regulates Metabolic Genes / positive regulation of protein localization to plasma membrane / Negative regulation of NOTCH4 signaling / positive regulation of insulin secretion / G alpha (z) signalling events / cellular response to prostaglandin E stimulus / melanosome / MAPK cascade / cellular response to hypoxia / peptidyl-serine phosphorylation / blood microparticle / positive regulation of canonical NF-kappaB signal transduction / DNA-binding transcription factor binding / vesicle / transmembrane transporter binding / positive regulation of MAPK cascade / protein kinase activity / intracellular signal transduction / cadherin binding / cell cycle / cell division / protein phosphorylation / focal adhesion / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / glutamatergic synapse / synapse / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Kostelecky, B. / Saurin, A.T. / Purkiss, A. / Parker, P.J. / McDonald, N.Q. | ||||||
Citation | Journal: Embo Rep. / Year: 2009 Title: Recognition of an Intra-Chain Tandem 14-3-3 Binding Site within Pkc Epsilon. Authors: Kostelecky, B. / Saurin, A.T. / Purkiss, A. / Parker, P.J. / Mcdonald, N.Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wh0.cif.gz | 180.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wh0.ent.gz | 141.3 KB | Display | PDB format |
PDBx/mmJSON format | 2wh0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/2wh0 ftp://data.pdbj.org/pub/pdb/validation_reports/wh/2wh0 | HTTPS FTP |
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-Related structure data
Related structure data | 1qjbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 27777.092 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PACYC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63104 #2: Protein/peptide | Mass: 3728.884 Da / Num. of mol.: 2 / Fragment: PKC EPSILON V3-DERIVED PEPTIDE, RESIDUES 342-372 / Source method: obtained synthetically / Details: SYNTHETIC FRAGMENT OF PKC EPSILON V3 REGION / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q02156, protein kinase C #3: Chemical | ChemComp-PGE / | #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.3 % / Description: NONE |
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Crystal grow | pH: 7.4 Details: 16 MG/ML PROTEIN 9% (W/V) POLYETHYLENE GLYCOL 3350, 25 MM CALCIUM ACETATE, 25 MM SODIUM FLUORIDE, pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 13, 2008 / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.441 |
Reflection | Resolution: 2.25→24.5 Å / Num. obs: 56277 / % possible obs: 99.4 % / Observed criterion σ(I): 3.9 / Redundancy: 4.9 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.25→2.45 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.9 / % possible all: 82.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QJB Resolution: 2.25→24.46 Å / σ(F): 1.99 / Phase error: 37.54 / Stereochemistry target values: TWIN_LSQ_F / Details: TWINNED REFINEMENT
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.57 Å2 / ksol: 0.35 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.93 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→24.46 Å
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Refine LS restraints |
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LS refinement shell |
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