+Open data
-Basic information
Entry | Database: PDB / ID: 6tm7 | ||||||
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Title | Human 14-3-3 sigma isoform in complex with PLP | ||||||
Components | 14-3-3 protein sigma | ||||||
Keywords | SIGNALING PROTEIN / human protein / h14-3-3sigma / complex / pyridoxal phosphate / PLP | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Tassone, G. / Pozzi, C. / Mangani, S. | ||||||
Funding support | 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2020 Title: Identification of Phosphate-Containing Compounds as New Inhibitors of 14-3-3/c-Abl Protein-Protein Interaction. Authors: Iralde-Lorente, L. / Tassone, G. / Clementi, L. / Franci, L. / Munier, C.C. / Cau, Y. / Mori, M. / Chiariello, M. / Angelucci, A. / Perry, M.W.D. / Pozzi, C. / Mangani, S. / Botta, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tm7.cif.gz | 101.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tm7.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 6tm7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/6tm7 ftp://data.pdbj.org/pub/pdb/validation_reports/tm/6tm7 | HTTPS FTP |
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-Related structure data
Related structure data | 6tlfC 6tlgC 1yz5S C: citing same article (ref.) S: Starting model for refinement |
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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: 31184.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Plasmid: pPROEX-HTb / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31947 #2: Chemical | #3: Chemical | ChemComp-PLP / | #4: Water | ChemComp-HOH / | 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: 4.56 Å3/Da / Density % sol: 73.05 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 40 % wt/vol PEG 4000, 600mM ammonium sulfate, 100 mM Tris-HCl, pH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 29, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 3→85.97 Å / Num. obs: 21085 / % possible obs: 99.4 % / Redundancy: 5 % / Biso Wilson estimate: 46.43 Å2 / Rmerge(I) obs: 0.198 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3016 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YZ5 Resolution: 3→78.65 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.883 / SU B: 17.779 / SU ML: 0.309 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.603 / ESU R Free: 0.37 / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 155.85 Å2 / Biso mean: 53.24 Å2 / Biso min: 13.43 Å2
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Refinement step | Cycle: final / Resolution: 3→78.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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