+Open data
-Basic information
Entry | Database: PDB / ID: 5n5r | |||||||||
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Title | 14-3-3 sigma in complex with TAZ pS89 peptide and fragment NV1 | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / 14-3-3 / TAZ / fragment / FBDD | |||||||||
Function / homology | Function and homology information kidney morphogenesis / regulation of metanephric nephron tubule epithelial cell differentiation / Physiological factors / RUNX3 regulates YAP1-mediated transcription / mesenchymal cell differentiation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / heart process / stem cell division / hippo signaling / tissue homeostasis ...kidney morphogenesis / regulation of metanephric nephron tubule epithelial cell differentiation / Physiological factors / RUNX3 regulates YAP1-mediated transcription / mesenchymal cell differentiation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / heart process / stem cell division / hippo signaling / tissue homeostasis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / glomerulus development / SMAD protein signal transduction / Signaling by Hippo / negative regulation of fat cell differentiation / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / RUNX2 regulates osteoblast differentiation / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / cilium assembly / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / positive regulation of osteoblast differentiation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of epithelial to mesenchymal transition / 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 / negative regulation of protein phosphorylation / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of protein kinase activity / multicellular organism growth / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of canonical Wnt signaling pathway / osteoblast differentiation / positive regulation of protein localization to nucleus / transcription corepressor activity / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cell growth / transcription regulator complex / transcription coactivator activity / nuclear body / protein ubiquitination / regulation of cell cycle / cadherin binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.801 Å | |||||||||
Authors | Sijbesma, E. / Leysen, S. / Ottmann, C. | |||||||||
Citation | Journal: Biochemistry / Year: 2017 Title: Identification of Two Secondary Ligand Binding Sites in 14-3-3 Proteins Using Fragment Screening. Authors: Sijbesma, E. / Skora, L. / Leysen, S. / Brunsveld, L. / Koch, U. / Nussbaumer, P. / Jahnke, W. / Ottmann, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n5r.cif.gz | 115.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n5r.ent.gz | 89 KB | Display | PDB format |
PDBx/mmJSON format | 5n5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/5n5r ftp://data.pdbj.org/pub/pdb/validation_reports/n5/5n5r | HTTPS FTP |
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-Related structure data
Related structure data | 5n5tC 5n5wC 5n75C 3mhrS 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
-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: 993.931 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9GZV5*PLUS |
-Non-polymers , 4 types, 279 molecules
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-NV1 / | #6: Water | ChemComp-HOH / | |
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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: 2.61 Å3/Da / Density % sol: 52.86 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 0.095M Na-HEPES pH 7.1, 28% PEG400, 0.19M Calcium chloride, 5% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 16, 2015 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.8→45.48 Å / Num. obs: 26488 / % possible obs: 98.1 % / Redundancy: 6.3 % / Biso Wilson estimate: 11.68 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.017 / Rrim(I) all: 0.043 / Net I/σ(I): 38.9 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MHR Resolution: 1.801→41.741 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.89 Å2 / Biso mean: 16.2629 Å2 / Biso min: 4.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.801→41.741 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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