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Yorodumi- PDB-8c2f: Structure of 14-3-3 sigma delta C with electrophilic peptide 3MHR-5 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c2f | ||||||
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Title | Structure of 14-3-3 sigma delta C with electrophilic peptide 3MHR-5 | ||||||
Components |
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Keywords | PROTEIN BINDING / 14-3-3 sigma / 3MHR-5 / covalent | ||||||
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 / 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 / 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: 2.3 Å | ||||||
Authors | van den Oetelaar, M.C.M. / Ottmann, C. | ||||||
Funding support | Netherlands, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: A simple method for developing lysine targeted covalent protein reagents. Authors: Gabizon, R. / Tivon, B. / Reddi, R.N. / van den Oetelaar, M.C.M. / Amartely, H. / Cossar, P.J. / Ottmann, C. / London, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c2f.cif.gz | 64.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c2f.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 8c2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/8c2f ftp://data.pdbj.org/pub/pdb/validation_reports/c2/8c2f | HTTPS FTP |
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-Related structure data
Related structure data | 8c2eC 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
-Protein / Protein/peptide , 2 types, 2 molecules AP
#1: Protein | Mass: 26542.914 Da / Num. of mol.: 1 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: 1151.190 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Cme = covalent crosslinker bound to the cysteine, which reacts with Lys122 of 14-3-3 sigma delta C Source: (synth.) Homo sapiens (human) |
-Non-polymers , 4 types, 64 molecules
#3: Chemical | ChemComp-TJI / | ||
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#4: Chemical | ChemComp-MG / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.08 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.095 M HEPES pH 7.1, 28% (v/v) PEG400 0.19 M CaCl2, 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: 1.03322 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03322 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→56.14 Å / Num. obs: 13362 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 11.64 Å2 / CC1/2: 0.98 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.3→2.38 Å / Num. unique obs: 1279 / CC1/2: 0.72 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→56.14 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.848 / SU B: 6.581 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.244 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.175 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→56.14 Å
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