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Yorodumi- PDB-6eww: Structure of 14-3-3 zeta in complex with CaMKK2 14-3-3 binding motif -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eww | ||||||
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Title | Structure of 14-3-3 zeta in complex with CaMKK2 14-3-3 binding motif | ||||||
Components |
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Keywords | SIGNALING PROTEIN / 14-3-3 protein / calcium/calmodulin-dependent protein kinase kinase 2 / CaMKK2 / phosphorylation | ||||||
Function / homology | Function and homology information Golgi reassembly / positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / CAMKK-AMPK signaling cascade / establishment of Golgi localization / Rap1 signalling / calmodulin-dependent protein kinase activity / regulation of protein kinase activity ...Golgi reassembly / positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / CAMKK-AMPK signaling cascade / establishment of Golgi localization / Rap1 signalling / calmodulin-dependent protein kinase activity / regulation of protein kinase activity / negative regulation of protein localization to nucleus / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CaMK IV-mediated phosphorylation of CREB / KSRP (KHSRP) binds and destabilizes mRNA / Activation of RAC1 downstream of NMDARs / GP1b-IX-V activation signalling / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / 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 / Activation of AMPK downstream of NMDARs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / negative regulation of innate immune response / regulation of ERK1 and ERK2 cascade / protein sequestering activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / calcium-mediated signaling / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / cellular response to reactive oxygen species / melanosome / MAPK cascade / protein tyrosine kinase activity / blood microparticle / DNA-binding transcription factor binding / vesicle / transmembrane transporter binding / protein autophosphorylation / calmodulin binding / neuron projection / cadherin binding / positive regulation of protein phosphorylation / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / ubiquitin protein ligase binding / calcium ion binding / negative regulation of apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / RNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.679 Å | ||||||
Authors | Lentini Santo, D. / Obsilova, V. / Obsil, T. | ||||||
Funding support | Czech Republic, 1items
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Citation | Journal: Biochim. Biophys. Acta / Year: 2018 Title: 14-3-3 protein directly interacts with the kinase domain of calcium/calmodulin-dependent protein kinase kinase (CaMKK2). Authors: Psenakova, K. / Petrvalska, O. / Kylarova, S. / Lentini Santo, D. / Kalabova, D. / Herman, P. / Obsilova, V. / Obsil, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eww.cif.gz | 185.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eww.ent.gz | 147.9 KB | Display | PDB format |
PDBx/mmJSON format | 6eww.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/6eww ftp://data.pdbj.org/pub/pdb/validation_reports/ew/6eww | HTTPS FTP |
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-Related structure data
Related structure data | 6felC 4fj3S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26511.961 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P63104 #2: Protein/peptide | Mass: 1112.198 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96RR4*PLUS #3: 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: 2.04 Å3/Da / Density % sol: 40.3 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion Details: PEG 2000, TRIS-HCl, HEPES, magnesium chloride, sodium fluoride, TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.679→47.89 Å / Num. obs: 26274 / % possible obs: 99.7 % / Redundancy: 6.42 % / CC1/2: 0.998 / Rrim(I) all: 0.08 / Net I/σ(I): 17.37 |
Reflection shell | Resolution: 2.679→2.84 Å / Redundancy: 6.23 % / Mean I/σ(I) obs: 5.21 / Num. unique obs: 4126 / CC1/2: 0.956 / Rrim(I) all: 0.3 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FJ3 Resolution: 2.679→47.712 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / Phase error: 22.36
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.679→47.712 Å
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Refine LS restraints |
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LS refinement shell |
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