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Yorodumi- PDB-7ob8: Crystal structure of 14-3-3 sigma in complex with LDB1 phosphopep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ob8 | ||||||
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Title | Crystal structure of 14-3-3 sigma in complex with LDB1 phosphopeptide and stabilizer Fusicoccin-A | ||||||
Components |
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Keywords | SIGNALING PROTEIN / 14-3-3 sigma protein-peptide-stabilizer complex | ||||||
Function / homology | Function and homology information Expression and translocation of olfactory receptors / regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / epithelial structure maintenance / beta-catenin-TCF complex / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / LIM domain binding ...Expression and translocation of olfactory receptors / regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / epithelial structure maintenance / beta-catenin-TCF complex / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / LIM domain binding / gastrulation with mouth forming second / Cardiogenesis / anterior/posterior axis specification / hair follicle development / regulation of focal adhesion assembly / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / cell leading edge / somatic stem cell population maintenance / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / positive regulation of cell adhesion / 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 / positive regulation of transcription elongation by RNA polymerase II / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / protein sequestering activity / protein kinase A signaling / negative regulation of innate immune response / protein export from nucleus / regulation of cell migration / 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 / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / neuron differentiation / Wnt signaling pathway / Regulation of expression of SLITs and ROBOs / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nervous system development / positive regulation of cell growth / DNA-binding transcription factor binding / transcription regulator complex / transcription coactivator activity / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / regulation of cell cycle / cell adhesion / cadherin binding / negative regulation of DNA-templated transcription / chromatin binding / chromatin / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol 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 | 7ob8.cif.gz | 136.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ob8.ent.gz | 86.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ob8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ob8_validation.pdf.gz | 848.6 KB | Display | wwPDB validaton report |
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Full document | 7ob8_full_validation.pdf.gz | 850.8 KB | Display | |
Data in XML | 7ob8_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 7ob8_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/7ob8 ftp://data.pdbj.org/pub/pdb/validation_reports/ob/7ob8 | HTTPS FTP |
-Related structure data
Related structure data | 7ob5C 7obcC 7obdC 7obgC 7obhC 7obkC 7oblC 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
-Protein / Protein/peptide , 2 types, 2 molecules AB
#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 BL21(DE3) (bacteria) / References: UniProt: P31947 |
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#2: Protein/peptide | Mass: 1257.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q86U70 |
-Non-polymers , 4 types, 348 molecules
#3: Chemical | ChemComp-FSC / | ||
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#4: Chemical | ChemComp-CL / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.45 Å3/Da / Density % sol: 49.72 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.095 M Hepes pH 7.1, 28%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 8, 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→41.66 Å / Num. obs: 27006 / % possible obs: 99.4 % / Redundancy: 6.1 % / Biso Wilson estimate: 12.39 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1208 / CC1/2: 0.936 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JC3 Resolution: 1.8→41.65 Å / SU ML: 0.1771 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 18.663 / 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: 17.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→41.65 Å
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Refine LS restraints |
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LS refinement shell |
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