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Yorodumi- PDB-6yoy: 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound... -
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-Basic information
Entry | Database: PDB / ID: 6yoy | ||||||
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Title | 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-025 | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / covalent fragment / p65 / 1433 | ||||||
Function / homology | Function and homology information acetaldehyde metabolic process / prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / cellular response to peptidoglycan / Regulated proteolysis of p75NTR / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 ...acetaldehyde metabolic process / prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / cellular response to peptidoglycan / Regulated proteolysis of p75NTR / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / CLEC7A/inflammasome pathway / negative regulation of protein sumoylation / defense response to tumor cell / postsynapse to nucleus signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to interleukin-6 / Interleukin-1 processing / actinin binding / cellular response to angiotensin / response to UV-B / NF-kappaB complex / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of leukocyte adhesion to vascular endothelial cell / Regulation of NFE2L2 gene expression / interleukin-1-mediated signaling pathway / vascular endothelial growth factor signaling pathway / toll-like receptor 4 signaling pathway / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / positive regulation of miRNA metabolic process / response to cobalamin / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of T cell receptor signaling pathway / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / non-canonical NF-kappaB signal transduction / phosphate ion binding / cellular response to lipoteichoic acid / TRAF6 mediated NF-kB activation / response to muramyl dipeptide / The NLRP3 inflammasome / Regulation of localization of FOXO transcription factors / general transcription initiation factor binding / keratinocyte proliferation / Transcriptional Regulation by VENTX / NF-kappaB binding / hair follicle development / phosphoserine residue binding / positive regulation of vascular endothelial growth factor production / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / neuropeptide signaling pathway / canonical NF-kappaB signal transduction / RNA polymerase II core promoter sequence-specific DNA binding / response to amino acid / cellular response to interleukin-1 / establishment of skin barrier / cellular defense response / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Purinergic signaling in leishmaniasis infection / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / response to cAMP / protein kinase A signaling / tumor necrosis factor-mediated signaling pathway / protein sequestering activity / response to muscle stretch / positive regulation of interleukin-12 production / negative regulation of innate immune response / negative regulation of insulin receptor signaling pathway / protein export from nucleus / NF-kB is activated and signals survival / CD209 (DC-SIGN) signaling / response to interleukin-1 / negative regulation of angiogenesis / : / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / negative regulation of miRNA transcription / liver development / positive regulation of interleukin-1 beta production / stem cell proliferation / response to cytokine / positive regulation of interleukin-8 production / response to ischemia / Translocation of SLC2A4 (GLUT4) to the plasma membrane / response to progesterone / Dectin-1 mediated noncanonical NF-kB signaling / negative regulation of extrinsic apoptotic signaling pathway / TP53 Regulates Metabolic Genes / Activation of NF-kappaB in B cells / animal organ morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Wolter, M. / Ottmann, C. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020 Title: Fragment-Based Stabilizers of Protein-Protein Interactions through Imine-Based Tethering. Authors: Wolter, M. / Valenti, D. / Cossar, P.J. / Levy, L.M. / Hristeva, S. / Genski, T. / Hoffmann, T. / Brunsveld, L. / Tzalis, D. / Ottmann, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yoy.cif.gz | 107.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yoy.ent.gz | 82.1 KB | Display | PDB format |
PDBx/mmJSON format | 6yoy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yoy_validation.pdf.gz | 750.4 KB | Display | wwPDB validaton report |
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Full document | 6yoy_full_validation.pdf.gz | 750.5 KB | Display | |
Data in XML | 6yoy_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 6yoy_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/6yoy ftp://data.pdbj.org/pub/pdb/validation_reports/yo/6yoy | HTTPS FTP |
-Related structure data
Related structure data | 6yowC 6yoxC 6yp2C 6yp3C 6yp8C 6yplC 6ypyC 6yq2C 6qhlS 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
#1: Protein | Mass: 26558.914 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: 1412.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q04206*PLUS |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-L3S / |
#5: 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: 2.45 Å3/Da / Density % sol: 49.89 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.095 M HEPES Na pH 7.1, 27% PEG400, 0.19M Calcium chloride, 5% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→41.27 Å / Num. obs: 26420 / % possible obs: 96.6 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.072 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.8→1.85 Å / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 4 / Num. unique obs: 1742 / CC1/2: 0.972 / Rrim(I) all: 0.262 / % possible all: 87.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6QHL Resolution: 1.8→41.27 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 24.41
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→41.27 Å
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Refine LS restraints |
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LS refinement shell |
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