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Yorodumi- PDB-7nye: 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nye | ||||||
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Title | 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-134 | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / benzaldehyde / covalent fragment / p65 / 1433 / RelA | ||||||
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 / 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: J.Med.Chem. / Year: 2021 Title: An Exploration of Chemical Properties Required for Cooperative Stabilization of the 14-3-3 Interaction with NF-kappa B-Utilizing a Reversible Covalent Tethering Approach. Authors: Wolter, M. / Valenti, D. / Cossar, P.J. / Hristeva, S. / Levy, L.M. / 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 | 7nye.cif.gz | 73.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nye.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 7nye.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nye_validation.pdf.gz | 882.3 KB | Display | wwPDB validaton report |
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Full document | 7nye_full_validation.pdf.gz | 886.6 KB | Display | |
Data in XML | 7nye_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 7nye_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/7nye ftp://data.pdbj.org/pub/pdb/validation_reports/ny/7nye | HTTPS FTP |
-Related structure data
Related structure data | 7bi3C 7biqC 7biwC 7biyC 7bjbC 7bjfC 7bjlC 7bjwC 7bkhC 7nj9C 7njbC 7nk3C 7nk5C 7nlaC 7nleC 7nm1C 7nm3C 7nm9C 7nmhC 7nr7C 7nv4C 7nviC 7nwsC 7nxsC 7nxtC 7nxwC 7nxyC 7ny4C 7nyfC 7nygC 7nz6C 7nzgC 7nzkC 7nzvC 7o34C 7o3aC 7o3fC 7o3pC 7o3qC 7o3rC 7o3sC 7o57C 7o59C 7o5aC 7o5cC 7o5dC 7o5fC 7o5gC 7o5oC 7o5pC 7o5sC 7o5uC 7o5xC 7o6fC 7o6gC 7o6iC 7o6jC 7o6kC 7o6mC 7o6oC 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 Details: the sequence follows an alternative sequencing (ID: CAA80524) Source: (synth.) Homo sapiens (human) / References: UniProt: Q04206 |
#3: Chemical | ChemComp-UVH / |
#4: Chemical | ChemComp-GOL / |
#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: 2.59 Å3/Da / Density % sol: 52.58 % / Mosaicity: 0 ° |
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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→41.82 Å / Num. obs: 57267 / % possible obs: 99.7 % / Redundancy: 12.8 % / Biso Wilson estimate: 12.1 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.037 / Rrim(I) all: 0.133 / Net I/σ(I): 17.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.41
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6QHL Resolution: 1.4→41.82 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.21 / Stereochemistry target values: ML / Details: MOLECULAR REPLACEMENT
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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: 68.19 Å2 / Biso mean: 17.6351 Å2 / Biso min: 6.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→41.82 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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