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Yorodumi- PDB-8c43: Ternary structure of 14-3-3sigma, strep-tagged PKA-responsive ERa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c43 | ||||||
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Title | Ternary structure of 14-3-3sigma, strep-tagged PKA-responsive ERa phosphopeptide, and Fusicoccin-A. | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / 14-3-3 / hub-protein / ERa F-domain phosphopeptide | ||||||
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 / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / protein kinase A signaling / 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: 1.4 Å | ||||||
Authors | Somsen, B.A. / Ottmann, C. | ||||||
Funding support | Netherlands, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Molecular basis and dual ligand regulation of tetrameric estrogen receptor alpha /14-3-3 zeta protein complex. Authors: Somsen, B.A. / Sijbesma, E. / Leysen, S. / Honzejkova, K. / Visser, E.J. / Cossar, P.J. / Obsil, T. / Brunsveld, L. / Ottmann, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c43.cif.gz | 75.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c43.ent.gz | 53.6 KB | Display | PDB format |
PDBx/mmJSON format | 8c43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/8c43 ftp://data.pdbj.org/pub/pdb/validation_reports/c4/8c43 | HTTPS FTP |
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-Related structure data
Related structure data | 8c3zC 8c40C 8c42C 4jc3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 at the beginning (-5 to -1) are part of the expression tag 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: 2080.199 Da / Num. of mol.: 1 / Mutation: F591R; P592R / Source method: obtained synthetically Details: This peptide is based on ERa residues 588-595 however with a C-terminal strep tag (PWSHQFEK) and two point mutations (F591R; P592R),This peptide is based on ERa residues 588-595 however with ...Details: This peptide is based on ERa residues 588-595 however with a C-terminal strep tag (PWSHQFEK) and two point mutations (F591R; P592R),This peptide is based on ERa residues 588-595 however with a C-terminal strep tag (PWSHQFEK) and two point mutations (F591R; P592R),This peptide is based on ERa residues 588-595 however with a C-terminal strep tag (PWSHQFEK) and two point mutations (F591R; P592R),This peptide is based on ERa residues 588-595 however with a C-terminal strep tag (PWSHQFEK) and two point mutations (F591R; P592R) Source: (synth.) Homo sapiens (human) | ||||||
#3: Chemical | #4: Chemical | ChemComp-SIT / | #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: 2.59 Å3/Da / Density % sol: 52.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.095 M Hepes pH 7.1, 0.19 M CaCl2, 25% PEG400, 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→45.34 Å / Num. obs: 53914 / % possible obs: 95.5 % / Redundancy: 13.9 % / CC1/2: 1 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.4→1.42 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2447 / CC1/2: 0.78 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JC3 Resolution: 1.4→45.34 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→45.34 Å
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Refine LS restraints |
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LS refinement shell |
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