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Yorodumi- PDB-6y1d: Binary complex of 14-3-3 sigma (C38N) with the Estrogen Related R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y1d | |||||||||
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Title | Binary complex of 14-3-3 sigma (C38N) with the Estrogen Related Receptor gamma (DBD) phosphopeptide | |||||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / 14-3-3 / ERRy phosphopeptide | |||||||||
Function / homology | Function and homology information AF-2 domain binding / nuclear steroid receptor activity / 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 ...AF-2 domain binding / nuclear steroid receptor activity / 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 / retinoic acid receptor signaling pathway / establishment of skin barrier / estrogen response element binding / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / intracellular steroid hormone receptor signaling pathway / 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 / steroid binding / 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 / Nuclear Receptor transcription pathway / nuclear receptor activity / intrinsic apoptotic signaling pathway in response to DNA damage / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / positive regulation of cell growth / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of cell cycle / DNA-binding transcription factor activity, RNA polymerase II-specific / cadherin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å | |||||||||
Authors | Somsen, B.A. / Ottmann, C. | |||||||||
Funding support | Netherlands, 2items
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Citation | Journal: Acs Chem.Biol. / Year: 2020 Title: Fluorescence Anisotropy-Based Tethering for Discovery of Protein-Protein Interaction Stabilizers. Authors: Sijbesma, E. / Somsen, B.A. / Miley, G.P. / Leijten-van de Gevel, I.A. / Brunsveld, L. / Arkin, M.R. / Ottmann, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y1d.cif.gz | 115.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y1d.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 6y1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/6y1d ftp://data.pdbj.org/pub/pdb/validation_reports/y1/6y1d | HTTPS FTP |
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-Related structure data
Related structure data | 6xxcC 6xy5C 6y18C 6y3wC 6y58C 3p1nS 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: 26553.875 Da / Num. of mol.: 1 / Mutation: C38N Source method: isolated from a genetically manipulated source 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: 1215.370 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide contains a C-terminal amide of which the nitrogen is represented as a seperate ligand. Source: (synth.) Homo sapiens (human) / References: UniProt: P62508*PLUS |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-CL / |
#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: 2.61 Å3/Da / Density % sol: 52.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.095 M HEPES (pH 7.3), 0.19 M CaCl2, 25% (v/v) PEG 400 and 5% (v/v) 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 PILATUS 6M-F / Detector: PIXEL / Date: Jun 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→66.29 Å / Num. obs: 59105 / % possible obs: 98.8 % / Redundancy: 12.3 % / CC1/2: 1 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 1.38→1.4 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2440 / CC1/2: 0.79 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3P1N Resolution: 1.38→45.618 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.53 Å2 / Biso mean: 18.7869 Å2 / Biso min: 6.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.38→45.618 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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