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Yorodumi- PDB-7bm9: Crystal structure of 14-3-3 sigma in complex with CIP2ApS904 peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bm9 | ||||||
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Title | Crystal structure of 14-3-3 sigma in complex with CIP2ApS904 peptide | ||||||
Components |
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Keywords | SIGNALING PROTEIN / protein-peptide complex | ||||||
Function / homology | Function and homology information 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 ...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 / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / 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 / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cell growth / regulation of cell cycle / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / 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: Acs Chem.Biol. / Year: 2022 Title: Fusicoccin-A Targets Cancerous Inhibitor of Protein Phosphatase 2A by Stabilizing a C-Terminal Interaction with 14-3-3. Authors: Brink, H.J. / van Senten, J.R. / De Vries-van Leeuwen, I.J. / da Costa Pereira, D. / Piersma, S.R. / Jimenez, C.R. / Centorrino, F. / Ottmann, C. / Siderius, M. / Smit, M.J. / de Boer, A.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bm9.cif.gz | 141.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bm9.ent.gz | 88.7 KB | Display | PDB format |
PDBx/mmJSON format | 7bm9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/7bm9 ftp://data.pdbj.org/pub/pdb/validation_reports/bm/7bm9 | HTTPS FTP |
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-Related structure data
Related structure data | 7bmcC 4jc3S 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: 624.621 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||||
#3: Chemical | ChemComp-CL / | ||||
#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: 2.52 Å3/Da / Density % sol: 51.25 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.095 M Hepes pH 7.1, 25% PEG 400, 0.19 M CaCl2 and 5% Glycerol |
-Data collection
Diffraction | Mean temperature: 298 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 1, 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→41.88 Å / Num. obs: 26877 / % possible obs: 98.2 % / Redundancy: 6.3 % / Biso Wilson estimate: 8.45 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 1251 / CC1/2: 0.929 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JC3 Resolution: 1.8→41.86 Å / SU ML: 0.1413 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 15.5594 / 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: 12.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→41.86 Å
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Refine LS restraints |
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LS refinement shell |
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