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Yorodumi- PDB-7o07: 14-3-3sigma covalently bound to peptide (chloroacetamide-Cys inte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o07 | |||||||||
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Title | 14-3-3sigma covalently bound to peptide (chloroacetamide-Cys interaction) | |||||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / 14-3-3 / covalent peptide binding / protein/peptide interaction | |||||||||
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: 1.2 Å | |||||||||
Authors | Somsen, B.A. / Ottmann, C. | |||||||||
Funding support | Netherlands, 1items
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Citation | Journal: Chem Sci / Year: 2021 Title: Covalent flexible peptide docking in Rosetta. Authors: Tivon, B. / Gabizon, R. / Somsen, B.A. / 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 | 7o07.cif.gz | 76 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o07.ent.gz | 54 KB | Display | PDB format |
PDBx/mmJSON format | 7o07.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/7o07 ftp://data.pdbj.org/pub/pdb/validation_reports/o0/7o07 | HTTPS FTP |
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-Related structure data
Related structure data | 5n75S S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 26542.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Initial 5 amino acids: GAMGS form the expression tag. The rest is the natural sequence. Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / Strain (production host): NiCo21(DE3) / References: UniProt: P31947 | ||||
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#2: Protein/peptide | Mass: 1324.790 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: FCA in this case stand for phenylalanine chloroacetamide. This is a non-natural amino acid similar to a phenylalanine with a parasubsituted chloroacetamide for covalent binding to the 14-3-3 ...Details: FCA in this case stand for phenylalanine chloroacetamide. This is a non-natural amino acid similar to a phenylalanine with a parasubsituted chloroacetamide for covalent binding to the 14-3-3 protein (Cys38). Furthermore this peptide contains a C-terminal amide and a N-terminal acetyl group. Source: (synth.) Homo sapiens (human) | ||||
#3: Chemical | ChemComp-MG / #4: 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: 2.66 Å3/Da / Density % sol: 53.73 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 0.095 M HEPES (pH 7.3), 0.19 M CaCl2, 26% (v/v) PEG 400 and 5% (v/v) glycerol 12 mg/mL 14-3-3sdc; 1:1.2 molar equivalents 14-3-3:peptide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96863 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96863 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→66.6 Å / Num. obs: 92037 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 0.998 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.2→1.22 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4524 / CC1/2: 0.785 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N75 Resolution: 1.2→45.8802 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.5 / 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: 57.1 Å2 / Biso mean: 16.7039 Å2 / Biso min: 6.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.2→45.8802 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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