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Yorodumi- PDB-7obl: Crystal structure of 14-3-3 sigma in complex with PKR phosphopept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7obl | ||||||
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Title | Crystal structure of 14-3-3 sigma in complex with PKR phosphopeptide and stabilizer Fusicoccin-A | ||||||
Components |
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Keywords | SIGNALING PROTEIN / 14-3-3 protein protein-peptide-stabilizer complex | ||||||
Function / homology | Function and homology information regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / eukaryotic translation initiation factor 2alpha kinase activity / response to interferon-alpha / positive regulation of stress-activated MAPK cascade / regulation of hematopoietic progenitor cell differentiation / negative regulation of osteoblast proliferation / protein phosphatase regulator activity / SUMOylation of immune response proteins / regulation of hematopoietic stem cell proliferation ...regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / eukaryotic translation initiation factor 2alpha kinase activity / response to interferon-alpha / positive regulation of stress-activated MAPK cascade / regulation of hematopoietic progenitor cell differentiation / negative regulation of osteoblast proliferation / protein phosphatase regulator activity / SUMOylation of immune response proteins / regulation of hematopoietic stem cell proliferation / regulation of hematopoietic stem cell differentiation / negative regulation of viral genome replication / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / antiviral innate immune response / 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 / endoplasmic reticulum unfolded protein response / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of chemokine production / RHO GTPases activate PKNs / cellular response to amino acid starvation / protein export from nucleus / negative regulation of innate immune response / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of cytokine production / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / non-specific protein-tyrosine kinase / response to virus / non-membrane spanning protein tyrosine kinase activity / PKR-mediated signaling / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / ISG15 antiviral mechanism / positive regulation of non-canonical NF-kappaB signal transduction / intrinsic apoptotic signaling pathway in response to DNA damage / Interferon alpha/beta signaling / double-stranded RNA binding / positive regulation of NF-kappaB transcription factor activity / kinase activity / positive regulation of cell growth / defense response to virus / negative regulation of translation / positive regulation of MAPK cascade / protein autophosphorylation / regulation of cell cycle / non-specific serine/threonine protein kinase / ribosome / protein kinase activity / cadherin binding / translation / negative regulation of cell population proliferation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / RNA binding / extracellular exosome / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Centorrino, F. / Andlovic, B. / Ottmann, C. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Cell Chem Biol / Year: 2023 Title: IFN alpha primes cancer cells for Fusicoccin-induced cell death via 14-3-3 PPI stabilization. Authors: Andlovic, B. / Heilmann, G. / Ninck, S. / Andrei, S.A. / Centorrino, F. / Higuchi, Y. / Kato, N. / Brunsveld, L. / Arkin, M. / Menninger, S. / Choidas, A. / Wolf, A. / Klebl, B. / Kaschani, ...Authors: Andlovic, B. / Heilmann, G. / Ninck, S. / Andrei, S.A. / Centorrino, F. / Higuchi, Y. / Kato, N. / Brunsveld, L. / Arkin, M. / Menninger, S. / Choidas, A. / Wolf, A. / Klebl, B. / Kaschani, F. / Kaiser, M. / Eickhoff, J. / Ottmann, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7obl.cif.gz | 139.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7obl.ent.gz | 87.7 KB | Display | PDB format |
PDBx/mmJSON format | 7obl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/7obl ftp://data.pdbj.org/pub/pdb/validation_reports/ob/7obl | HTTPS FTP |
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-Related structure data
Related structure data | 7ob5C 7ob8C 7obcC 7obdC 7obgC 7obhC 7obkC 7obsC 7obtC 7obxC 7obyC 4jc3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 28210.518 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 BL21(DE3) (bacteria) / References: UniProt: P31947 | ||||
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#2: Protein/peptide | Mass: 1412.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: P19525, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase | ||||
#3: Chemical | ChemComp-FSC / | ||||
#4: Chemical | #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: 2.45 Å3/Da / Density % sol: 49.83 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.095 M Hepes pH7.3, 25%PEG 400, 0.19 M CaCl2 and 5 % Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5419 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Sep 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→34.49 Å / Num. obs: 27265 / % possible obs: 98.8 % / Redundancy: 6 % / Biso Wilson estimate: 8.27 Å2 / CC1/2: 0.947 / Rpim(I) all: 0.154 / Net I/σ(I): 5 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1101 / CC1/2: 0.91 / R split: 0.258 / % possible all: 80.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JC3 Resolution: 1.8→34.48 Å / SU ML: 0.2183 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.8732 / Stereochemistry target values: GeoStd + Monomer Library
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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: 11.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→34.48 Å
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Refine LS restraints |
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LS refinement shell |
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