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Open data
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Basic information
Entry | Database: PDB / ID: 6y3v | ||||||
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Title | 14-3-3 Sigma in complex with phosphorylated c-Jun peptide | ||||||
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![]() | PROTEIN BINDING / 14-3-3 / c-Jun / complex / protein / protein-protein interactions | ||||||
Function / homology | ![]() cAMP response element binding / transcription factor AP-1 complex / integrated stress response signaling / positive regulation of DNA-templated transcription initiation / release from viral latency / WNT5:FZD7-mediated leishmania damping / SMAD protein signal transduction / positive regulation by host of viral transcription / nuclear chromosome / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models ...cAMP response element binding / transcription factor AP-1 complex / integrated stress response signaling / positive regulation of DNA-templated transcription initiation / release from viral latency / WNT5:FZD7-mediated leishmania damping / SMAD protein signal transduction / positive regulation by host of viral transcription / nuclear chromosome / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / negative regulation of DNA binding / Activation of the AP-1 family of transcription factors / ubiquitin-like protein ligase binding / R-SMAD binding / Regulation of localization of FOXO transcription factors / general transcription initiation factor binding / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation by host of viral transcription / 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 / positive regulation of vascular associated smooth muscle cell proliferation / protein sequestering activity / protein kinase A signaling / cellular response to cadmium ion / negative regulation of innate immune response / protein export from nucleus / response to endoplasmic reticulum stress / GTPase activator activity / transforming growth factor beta receptor signaling pathway / 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 / Regulation of PTEN gene transcription / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Transcription of DNA Repair Genes / TP53 Regulates Metabolic Genes / FCERI mediated MAPK activation / negative regulation of protein kinase activity / MAPK6/MAPK4 signaling / euchromatin / DNA-binding transcription repressor activity, RNA polymerase II-specific / Pre-NOTCH Transcription and Translation / positive regulation of miRNA transcription / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cellular response to reactive oxygen species / RNA polymerase II transcription regulator complex / intrinsic apoptotic signaling pathway in response to DNA damage / sequence-specific double-stranded DNA binding / protein localization / Signaling by ALK fusions and activated point mutants / regulation of cell population proliferation / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / DNA-binding transcription activator activity, RNA polymerase II-specific / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / regulation of cell cycle / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / cadherin binding / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ballone, A. / Lau, R.A. / Zweipfenning, F.P.A. / Ottmann, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A new soaking procedure for X-ray crystallographic structural determination of protein-peptide complexes. Authors: Ballone, A. / Lau, R.A. / Zweipfenning, F.P.A. / Ottmann, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76 KB | Display | ![]() |
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PDB format | ![]() | 52.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6y3mC ![]() 6y3oC ![]() 6y3rC ![]() 6y3sC ![]() 6y40C ![]() 6y44C ![]() 6y8aC ![]() 6y8bC ![]() 6y8dC ![]() 6y8eC ![]() 3lw1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() | ||||||
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#2: Protein/peptide | Mass: 1502.725 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P05412*PLUS | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.17 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 28% (v/v) PEG400, 1.25% glycerol, 0.2M CaCl, 0.1M HEPES pH 7.5, 2mM BME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.499→66.531 Å / Num. obs: 46803 / % possible obs: 99 % / Redundancy: 11.9 % / Biso Wilson estimate: 11.52 Å2 / CC1/2: 0.483 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 1.5→1.53 Å / Num. unique obs: 2252 / CC1/2: 0.289 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3LW1 Resolution: 1.499→66.531 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.499→66.531 Å
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Refine LS restraints |
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LS refinement shell |
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