+Open data
-Basic information
Entry | Database: PDB / ID: 6tlg | ||||||
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Title | Ligand-free state of human 14-3-3 sigma isoform | ||||||
Components | 14-3-3 protein sigma | ||||||
Keywords | SIGNALING PROTEIN / human protein / 14-3-3 / sigma isoform / h14-3-3sigma | ||||||
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 / 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 / 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 / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 | 6tlg.cif.gz | 63 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tlg.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 6tlg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tlg_validation.pdf.gz | 452.8 KB | Display | wwPDB validaton report |
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Full document | 6tlg_full_validation.pdf.gz | 454.6 KB | Display | |
Data in XML | 6tlg_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 6tlg_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/6tlg ftp://data.pdbj.org/pub/pdb/validation_reports/tl/6tlg | HTTPS FTP |
-Related structure data
Related structure data | 6tlfC 6tm7C 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.: 1 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 | ||||
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#2: Chemical | ChemComp-PEG / | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.49 Å3/Da / Density % sol: 72.64 % |
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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: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 17, 2017 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→86.44 Å / Num. obs: 19842 / % possible obs: 96.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 39.6 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.056 / Rrim(I) all: 0.122 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2964 / CC1/2: 0.908 / Rpim(I) all: 0.216 / Rrim(I) all: 0.461 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YZ5 Resolution: 2.4→58.92 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.087 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.199 / 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: 165.09 Å2 / Biso mean: 56.932 Å2 / Biso min: 25.82 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3716 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→58.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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