+Open data
-Basic information
Entry | Database: PDB / ID: 5oeh | |||||||||
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Title | Molecular tweezers modulate 14-3-3 protein-protein interactions. | |||||||||
Components | 14-3-3 protein sigma | |||||||||
Keywords | SIGNALING PROTEIN / 14-3-3 Protein / Inhibition / supramolecular ligands | |||||||||
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 / molecular replacement / Resolution: 2.35 Å | |||||||||
Authors | Bier, D. / Ottmann, C. | |||||||||
Citation | Journal: Nat Chem / Year: 2013 Title: Molecular tweezers modulate 14-3-3 protein-protein interactions. Authors: Bier, D. / Rose, R. / Bravo-Rodriguez, K. / Bartel, M. / Ramirez-Anguita, J.M. / Dutt, S. / Wilch, C. / Klarner, F.G. / Sanchez-Garcia, E. / Schrader, T. / Ottmann, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oeh.cif.gz | 63.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oeh.ent.gz | 44.8 KB | Display | PDB format |
PDBx/mmJSON format | 5oeh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/5oeh ftp://data.pdbj.org/pub/pdb/validation_reports/oe/5oeh | HTTPS FTP |
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-Related structure data
Related structure data | 5oegC 3lw1S 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
#1: Protein | Mass: 26542.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GAMGS - cleavage artifact / Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947 |
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#2: Chemical | ChemComp-9SZ / ( |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.41 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion Details: 0.09 M HEPES sodium salt, 1.26 M Tri-Sodium Citrate, 10 % Glycerol, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.35→45.54 Å / Num. obs: 15745 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.199 % / Biso Wilson estimate: 58.097 Å2 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.059 / Χ2: 0.944 / Net I/σ(I): 22.44 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LW1 Resolution: 2.35→45.54 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.835 / SU ML: 0.16 / SU R Cruickshank DPI: 0.2478 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.226 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 101.62 Å2 / Biso mean: 53.748 Å2 / Biso min: 36.42 Å2
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Refinement step | Cycle: final / Resolution: 2.35→45.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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