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Yorodumi- PDB-6y6b: Crystal structure of human 14-3-3 gamma in complex with CaMKK2 14... -
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-Basic information
Entry | Database: PDB / ID: 6y6b | |||||||||
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Title | Crystal structure of human 14-3-3 gamma in complex with CaMKK2 14-3-3 binding motif Ser100 and 16-OMe-Fusicoccin H | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / 14-3-3 protein / complex / CaMKK / Fusicoccin | |||||||||
Function / homology | Function and homology information positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / regulation of protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / calcium/calmodulin-dependent protein kinase activity / regulation of neuron differentiation / CaMK IV-mediated phosphorylation of CREB / Activation of RAC1 downstream of NMDARs / protein kinase C inhibitor activity ...positive regulation of autophagy of mitochondrion / Ca2+/calmodulin-dependent protein kinase / CAMKK-AMPK signaling cascade / regulation of protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / calcium/calmodulin-dependent protein kinase activity / regulation of neuron differentiation / CaMK IV-mediated phosphorylation of CREB / Activation of RAC1 downstream of NMDARs / protein kinase C inhibitor activity / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / regulation of signal transduction / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cellular response to glucose starvation / 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 / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / negative regulation of TORC1 signaling / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein sequestering activity / AURKA Activation by TPX2 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / calcium-mediated signaling / TP53 Regulates Metabolic Genes / protein kinase C binding / insulin-like growth factor receptor binding / negative regulation of protein kinase activity / regulation of synaptic plasticity / receptor tyrosine kinase binding / cellular response to reactive oxygen species / cellular response to insulin stimulus / Regulation of PLK1 Activity at G2/M Transition / MAPK cascade / presynapse / protein tyrosine kinase activity / protein autophosphorylation / calmodulin binding / neuron projection / positive regulation of protein phosphorylation / protein domain specific binding / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / calcium ion binding / positive regulation of DNA-templated transcription / signal transduction / RNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å | |||||||||
Authors | Lentini Santo, D. / Obsilova, V. / Obsil, T. | |||||||||
Funding support | Czech Republic, 2items
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Citation | Journal: Acs Chem.Biol. / Year: 2020 Title: Stabilization of Protein-Protein Interactions between CaMKK2 and 14-3-3 by Fusicoccins. Authors: Lentini Santo, D. / Petrvalska, O. / Obsilova, V. / Ottmann, C. / Obsil, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y6b.cif.gz | 127.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y6b.ent.gz | 79.7 KB | Display | PDB format |
PDBx/mmJSON format | 6y6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y6b_validation.pdf.gz | 761.3 KB | Display | wwPDB validaton report |
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Full document | 6y6b_full_validation.pdf.gz | 763.9 KB | Display | |
Data in XML | 6y6b_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 6y6b_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/6y6b ftp://data.pdbj.org/pub/pdb/validation_reports/y6/6y6b | HTTPS FTP |
-Related structure data
Related structure data | 6y4kC 2b05S 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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Unit cell |
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-Components
#1: Protein | Mass: 27199.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61981 #2: Protein/peptide | Mass: 1112.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: Q96RR4, Ca2+/calmodulin-dependent protein kinase #3: Chemical | ChemComp-OD8 / ( | Has ligand of interest | N | |
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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: 4.76 Å3/Da / Density % sol: 74.18 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG400, HEPES, magnesium chloride, hexafluoropropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 3.08→48.99 Å / Num. obs: 20904 / % possible obs: 99.9 % / Redundancy: 21.72 % / Biso Wilson estimate: 110.21 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.28 / Net I/σ(I): 11.53 |
Reflection shell | Resolution: 3.08→3.26 Å / Redundancy: 22 % / Mean I/σ(I) obs: 0.69 / Num. unique obs: 3285 / CC1/2: 0.226 / Rrim(I) all: 4.97 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B05 Resolution: 3.08→17.75 Å / SU ML: 0.4663 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.9508 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 113.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.08→17.75 Å
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Refine LS restraints |
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LS refinement shell |
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