+Open data
-Basic information
Entry | Database: PDB / ID: 7nix | |||||||||
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Title | 14-3-3 sigma with AS160 binding site pT642 | |||||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / 1433 / TBC1 domain family member 4 / peptide-protein complex | |||||||||
Function / homology | Function and homology information negative regulation of vesicle fusion / 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 vesicle fusion / 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 / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / vesicle-mediated transport / protein sequestering activity / protein kinase A signaling / negative regulation of innate immune response / protein export from nucleus / GTPase activator 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 / cellular response to insulin stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / positive regulation of cell growth / vesicle / 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 / molecular replacement / Resolution: 1.9 Å | |||||||||
Authors | Wolter, M. / Ottmann, C. | |||||||||
Funding support | 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2021 Title: Reversible Covalent Imine-Tethering for Selective Stabilization of 14-3-3 Hub Protein Interactions. Authors: Cossar, P.J. / Wolter, M. / van Dijck, L. / Valenti, D. / Levy, L.M. / Ottmann, C. / Brunsveld, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nix.cif.gz | 109.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nix.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 7nix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/7nix ftp://data.pdbj.org/pub/pdb/validation_reports/ni/7nix | HTTPS FTP |
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-Related structure data
Related structure data | 7aogC 7axnC 7ayfC 7az1C 7az2C 7bdpC 7bdtC 7bdyC 7bfwC 7bg3C 7bgqC 7bgrC 7bgvC 7bgwC 7nifC 7nigC 7nj6C 7nj8C 7njaC 7nqpC 7nrkC 7nrlC 7nsvC 4jddS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28210.518 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: 1446.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O60343 | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-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: 53.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 40% (v/v) MPD, 100 mM CHES/ Sodium hydroxide pH 9.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976284 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 28, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976284 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→104.98 Å / Num. obs: 25949 / % possible obs: 100 % / Redundancy: 37.5 % / Biso Wilson estimate: 29.31 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.017 / Rrim(I) all: 0.105 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 38.7 % / Rmerge(I) obs: 1.55 / Num. unique obs: 1623 / CC1/2: 0.97 / Rpim(I) all: 0.252 / Rrim(I) all: 1.57 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JDD Resolution: 1.9→60.61 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.44 / 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: 115.06 Å2 / Biso mean: 37.2096 Å2 / Biso min: 15.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→60.61 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17 / % reflection obs: 100 %
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