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- PDB-3smk: Crystal structure of human 14-3-3 sigma C38V/N166H in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3smk | ||||||
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Title | Crystal structure of human 14-3-3 sigma C38V/N166H in complex with TASK-3 peptide and stabilizer Cotylenin A | ||||||
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![]() | PEPTIDE BINDING PROTEIN / Helical protein / Phosphoprotein / Adapter protein | ||||||
Function / homology | ![]() TWIK-releated acid-sensitive K+ channel (TASK) / Phase 4 - resting membrane potential / stabilization of membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization ...TWIK-releated acid-sensitive K+ channel (TASK) / Phase 4 - resting membrane potential / stabilization of membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / potassium channel activity / potassium ion import across plasma membrane / 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 / potassium ion transmembrane transport / protein kinase A signaling / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / potassium ion transport / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / synaptic vesicle / 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 / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Anders, C. / Schumacher, B. / Ottmann, C. | ||||||
![]() | ![]() Title: A semisynthetic fusicoccane stabilizes a protein-protein interaction and enhances the expression of K+ channels at the cell surface. Authors: Anders, C. / Higuchi, Y. / Koschinsky, K. / Bartel, M. / Schumacher, B. / Thiel, P. / Nitta, H. / Preisig-Muller, R. / Schlichthorl, G. / Renigunta, V. / Ohkanda, J. / Daut, J. / Kato, N. / Ottmann, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.5 KB | Display | ![]() |
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PDB format | ![]() | 49.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 798.3 KB | Display | ![]() |
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Full document | ![]() | 804.9 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3p1nC ![]() 3p1oC ![]() 3p1pC ![]() 3p1qC ![]() 3p1rC ![]() 3p1sC ![]() 3smlC ![]() 3smmC ![]() 3smnC ![]() 3smoC ![]() 3sp5C ![]() 3sprC ![]() 3ux0C ![]() 4fr3C ![]() 3lw1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 26562.947 Da / Num. of mol.: 1 / Mutation: C38V N166H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 856.950 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) ![]() |
#3: Chemical | ChemComp-CW7 / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.095M HEPES Na-Salt pH7.4, 25.6% PEG 400, 0.19M CaCl2, 5% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 8, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Number: 67249 / Rmerge(I) obs: 0.064 / D res high: 2.1 Å / Num. obs: 17095 / % possible obs: 99.6 | ||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.1→19.34 Å / Num. all: 17156 / Num. obs: 17095 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.93 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.64 | ||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 3LW1 Resolution: 2.1→19.34 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.664 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.207 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→19.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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