+Open data
-Basic information
Entry | Database: PDB / ID: 6qhm | ||||||
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Title | 14-3-3 sigma with RelA/p65 binding site pS281 | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / 14-3-3 / 14-3-3 sigma / p65 / 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 / 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 / actinin binding / NF-kappaB complex / negative regulation of non-canonical NF-kappaB signal transduction / cellular response to angiotensin / response to UV-B / interleukin-1-mediated signaling pathway / vascular endothelial growth factor signaling pathway / Regulation of NFE2L2 gene expression / positive regulation of leukocyte adhesion to vascular endothelial cell / positive regulation of miRNA metabolic process / toll-like receptor 4 signaling pathway / 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 / phosphoserine residue binding / neuropeptide signaling pathway / 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 / canonical NF-kappaB signal transduction / establishment of skin barrier / response to amino acid / cellular response to interleukin-1 / 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 / negative regulation of insulin receptor signaling pathway / response to cAMP / tumor necrosis factor-mediated signaling pathway / response to muscle stretch / protein export from nucleus / negative regulation of innate immune response / NF-kB is activated and signals survival / positive regulation of interleukin-12 production / CD209 (DC-SIGN) signaling / response to interleukin-1 / 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 / response to ischemia / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of interleukin-8 production / 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 / Resolution: 1.25 Å | ||||||
Authors | Wolter, M. / Ottmann, C. | ||||||
Funding support | Netherlands, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2020 Title: Selectivity via Cooperativity: Preferential Stabilization of the p65/14-3-3 Interaction with Semisynthetic Natural Products. Authors: Wolter, M. / de Vink, P. / Neves, J.F. / Srdanovic, S. / Higuchi, Y. / Kato, N. / Wilson, A. / Landrieu, I. / Brunsveld, L. / Ottmann, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qhm.cif.gz | 164.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qhm.ent.gz | 131 KB | Display | PDB format |
PDBx/mmJSON format | 6qhm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/6qhm ftp://data.pdbj.org/pub/pdb/validation_reports/qh/6qhm | HTTPS FTP |
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-Related structure data
Related structure data | 6nv2C 6qhlC 3mhrS 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: 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: 1645.659 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q04206*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.095 M HEPES Na pH 7.1, 28% 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: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03322 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03322 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→62.57 Å / Num. obs: 80102 / % possible obs: 99.9 % / Redundancy: 8.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.079 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.25→1.27 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.744 / Num. unique obs: 4152 / CC1/2: 0.723 / Rrim(I) all: 0.88 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MHR Resolution: 1.25→55.97 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.69
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→55.97 Å
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Refine LS restraints |
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LS refinement shell |
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