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Yorodumi- PDB-7njb: 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7njb | ||||||
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Title | 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-132 | ||||||
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 / Regulated proteolysis of p75NTR / cellular response to peptidoglycan / 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 / Regulated proteolysis of p75NTR / cellular response to peptidoglycan / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / CLEC7A/inflammasome pathway / SUMOylation of immune response proteins / negative regulation of protein sumoylation / nucleotide-binding oligomerization domain containing 2 signaling pathway / postsynapse to nucleus signaling pathway / defense response to tumor cell / Interleukin-1 processing / cellular response to interleukin-6 / negative regulation of non-canonical NF-kappaB signal transduction / actinin binding / NF-kappaB complex / cellular response to angiotensin / response to UV-B / interleukin-1-mediated signaling pathway / vascular endothelial growth factor signaling pathway / toll-like receptor 4 signaling pathway / Regulation of NFE2L2 gene expression / positive regulation of leukocyte adhesion to vascular endothelial cell / positive regulation of miRNA metabolic process / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / positive regulation of T cell receptor signaling pathway / response to cobalamin / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / phosphate ion binding / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation / cellular response to lipoteichoic acid / 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 / neuropeptide signaling pathway / phosphoserine residue binding / positive regulation of vascular endothelial growth factor production / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / RNA polymerase II core promoter sequence-specific DNA binding / establishment of skin barrier / response to amino acid / cellular response to interleukin-1 / canonical NF-kappaB signal transduction / cellular defense response / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Purinergic signaling in leishmaniasis infection / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / response to cAMP / negative regulation of insulin receptor signaling pathway / tumor necrosis factor-mediated signaling pathway / response to muscle stretch / protein export from nucleus / NF-kB is activated and signals survival / positive regulation of interleukin-12 production / CD209 (DC-SIGN) signaling / response to interleukin-1 / negative regulation of innate immune response / negative regulation of angiogenesis / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / negative regulation of miRNA transcription / response to progesterone / liver development / response to organic substance / 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 / 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 / peptide binding / animal organ morphogenesis 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 | 7njb.cif.gz | 73.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7njb.ent.gz | 51.3 KB | Display | PDB format |
PDBx/mmJSON format | 7njb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/7njb ftp://data.pdbj.org/pub/pdb/validation_reports/nj/7njb | HTTPS FTP |
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-Related structure data
Related structure data | 7bi3C 7biqC 7biwC 7biyC 7bjbC 7bjfC 7bjlC 7bjwC 7bkhC 7nj9C 7nk3C 7nk5C 7nlaC 7nleC 7nm1C 7nm3C 7nm9C 7nmhC 7nr7C 7nv4C 7nviC 7nwsC 7nxsC 7nxtC 7nxwC 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 (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 on special symmetry positions |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AP
#1: Protein | Mass: 28226.518 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 / Mutation: E49R / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q04206 |
-Non-polymers , 4 types, 333 molecules
#3: Chemical | ChemComp-GOL / |
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#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-UG8 / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.52 % / 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→66.42 Å / Num. obs: 57285 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 13.24 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.038 / Rrim(I) all: 0.137 / Net I/σ(I): 14.3 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 99.9
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6QHL Resolution: 1.4→41.74 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.16 / 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: 60.63 Å2 / Biso mean: 18.8584 Å2 / Biso min: 7.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→41.74 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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