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- PDB-7nxw: 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7nxw | ||||||
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Title | 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-182 | ||||||
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![]() | PEPTIDE BINDING PROTEIN / benzaldehyde / covalent fragment / p65 / 1433 / RelA | ||||||
Function / homology | ![]() 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 / NF-kappaB complex / response to UV-B / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of leukocyte adhesion to vascular endothelial cell / interleukin-1-mediated signaling pathway / Regulation of NFE2L2 gene expression / 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 / positive regulation of T cell receptor signaling pathway / regulation of epidermal cell division / protein kinase C inhibitor activity / 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 / neuropeptide signaling pathway / negative regulation of keratinocyte proliferation / canonical NF-kappaB signal transduction / RNA polymerase II core promoter sequence-specific DNA binding / response to amino acid / establishment of skin barrier / cellular response to interleukin-1 / 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 / protein export from nucleus / negative regulation of insulin receptor signaling pathway / 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 / stem cell proliferation / positive regulation of interleukin-1 beta production / response to cytokine / positive regulation of interleukin-8 production / Translocation of SLC2A4 (GLUT4) to the plasma membrane / response to ischemia / 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 / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / peptide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Wolter, M. / Ottmann, C. | ||||||
Funding support | 1items
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.1 KB | Display | ![]() |
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PDB format | ![]() | 49.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 679.4 KB | Display | ![]() |
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Full document | ![]() | 681.5 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | 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 ![]() 7nxyC ![]() 7ny4C ![]() 7nyeC ![]() 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 ( |
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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
-Protein / Protein/peptide , 2 types, 2 molecules AP
#1: Protein | Mass: 26558.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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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.) ![]() |
-Non-polymers , 5 types, 272 molecules ![](data/chem/img/UVZ.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-UVZ / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-MG / | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.3 % / 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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 27, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976284 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→66.35 Å / Num. obs: 90329 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 13.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.013 / Rrim(I) all: 0.045 / Net I/σ(I): 25.9 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR | R rigid body: 0.446
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6QHL Resolution: 1.2→56.19 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.15 / 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: 52.45 Å2 / Biso mean: 17.6561 Å2 / Biso min: 9.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.2→56.19 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %
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