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Yorodumi- PDB-6y8a: 14-3-3 Sigma in complex with phosphorylated camkk2{pS511} peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y8a | ||||||
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Title | 14-3-3 Sigma in complex with phosphorylated camkk2{pS511} peptide | ||||||
Components |
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Keywords | PROTEIN BINDING / 14-3-3 / camkk2{pS511} / complex / protein / protein-protein interactions | ||||||
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 / CaMK IV-mediated phosphorylation of CREB / Activation of RAC1 downstream of NMDARs / regulation of epidermal cell division / 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 / CaMK IV-mediated phosphorylation of CREB / Activation of RAC1 downstream of NMDARs / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / 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 / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / protein kinase A signaling / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / calcium-mediated signaling / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / cellular response to reactive oxygen species / intrinsic apoptotic signaling pathway in response to DNA damage / MAPK cascade / positive regulation of cell growth / protein tyrosine kinase activity / protein autophosphorylation / calmodulin binding / regulation of cell cycle / cadherin binding / neuron projection / positive regulation of protein phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Ballone, A. / Lau, R.A. / Zweipfenning, F.P.A. / Ottmann, C. | ||||||
Funding support | Netherlands, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2020 Title: A new soaking procedure for X-ray crystallographic structural determination of protein-peptide complexes. Authors: Ballone, A. / Lau, R.A. / Zweipfenning, F.P.A. / Ottmann, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y8a.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y8a.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 6y8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y8a_validation.pdf.gz | 434.2 KB | Display | wwPDB validaton report |
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Full document | 6y8a_full_validation.pdf.gz | 435.4 KB | Display | |
Data in XML | 6y8a_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 6y8a_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/6y8a ftp://data.pdbj.org/pub/pdb/validation_reports/y8/6y8a | HTTPS FTP |
-Related structure data
Related structure data | 6y3mC 6y3oC 6y3rC 6y3sC 6y3vC 6y40C 6y44C 6y8bC 6y8dC 6y8eC 3lw1S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28226.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947 | ||||||
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#2: Protein/peptide | Mass: 881.849 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: Q96RR4, Ca2+/calmodulin-dependent protein kinase | ||||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | 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: 2.65 Å3/Da / Density % sol: 53.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 28% PEG400, 5% glycerol, 0.2M CaCl, 0.1M HEPES pH 7.5, 2mM BME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.973 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 28, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.973 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→29.325 Å / Num. obs: 45770 / % possible obs: 96.5 % / Redundancy: 11.1 % / Biso Wilson estimate: 15.88 Å2 / CC1/2: 0.999 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 1.5→1.53 Å / Num. unique obs: 1763 / CC1/2: 0.87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LW1 Resolution: 1.5→29.325 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→29.325 Å
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Refine LS restraints |
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LS refinement shell |
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