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Yorodumi- PDB-6ypy: 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ypy | ||||||
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Title | 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-123 | ||||||
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 / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / Regulated proteolysis of p75NTR ...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 / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / Regulated proteolysis of p75NTR / 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 / negative regulation of non-canonical NF-kappaB signal transduction / actinin binding / cellular response to angiotensin / response to UV-B / NF-kappaB complex / 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 / positive regulation of miRNA metabolic process / non-canonical NF-kappaB signal transduction / toll-like receptor 4 signaling pathway / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / 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 / phosphate ion binding / cellular response to lipoteichoic acid / response to muramyl dipeptide / TRAF6 mediated NF-kB activation / The NLRP3 inflammasome / Regulation of localization of FOXO transcription factors / general transcription initiation factor binding / keratinocyte proliferation / neuropeptide signaling pathway / Transcriptional Regulation by VENTX / phosphoserine residue binding / NF-kappaB binding / hair follicle development / cellular response to interleukin-1 / positive regulation of vascular endothelial growth factor production / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / response to amino acid / RNA polymerase II core promoter sequence-specific DNA binding / 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 / canonical NF-kappaB signal transduction / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / antiviral innate immune response / negative regulation of insulin receptor signaling pathway / tumor necrosis factor-mediated signaling pathway / response to cAMP / protein sequestering activity / protein kinase A signaling / response to muscle stretch / positive regulation of interleukin-12 production / negative regulation of innate immune response / protein export from nucleus / CD209 (DC-SIGN) signaling / NF-kB is activated and signals survival / response to interleukin-1 / negative regulation of angiogenesis / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / negative regulation of miRNA transcription / positive regulation of protein export from nucleus / liver development / stem cell proliferation / positive regulation of interleukin-1 beta production / response to cytokine / positive regulation of interleukin-8 production / response to ischemia / response to progesterone / Translocation of SLC2A4 (GLUT4) to the plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / Dectin-1 mediated noncanonical NF-kB signaling / TP53 Regulates Metabolic Genes / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / Activation of NF-kappaB in B cells / negative regulation of protein kinase activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 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 | 6ypy.cif.gz | 73.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ypy.ent.gz | 51.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ypy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/6ypy ftp://data.pdbj.org/pub/pdb/validation_reports/yp/6ypy | HTTPS FTP |
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-Related structure data
Related structure data | 6yowC 6yoxC 6yoyC 6yp2C 6yp3C 6yp8C 6yplC 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-P7E / |
#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: 2.6 Å3/Da / Density % sol: 52.63 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1 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: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 18, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→56.22 Å / Num. obs: 57549 / % possible obs: 100 % / Redundancy: 1.9 % / Biso Wilson estimate: 10.05 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.046 / Rrim(I) all: 0.065 / Net I/σ(I): 11.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.42
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6QHL Resolution: 1.4→34.465 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.75
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.34 Å2 / Biso mean: 15.4074 Å2 / Biso min: 5.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→34.465 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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