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Yorodumi- PDB-6nv2: 14-3-3 sigma with RelA/p65 binding site pS45 in complex with DP005 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nv2 | ||||||
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Title | 14-3-3 sigma with RelA/p65 binding site pS45 in complex with DP005 | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / fusicoccanes / natural products / 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 / response to cobalamin / positive regulation of Schwann cell differentiation / 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 / response to cobalamin / 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 / hair follicle development / 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 / 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 / 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 / negative regulation of angiogenesis / 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 / negative regulation of miRNA transcription / 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 / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of miRNA transcription / positive regulation of protein export from nucleus / liver development / peptide binding / stem cell proliferation / positive regulation of interleukin-1 beta production / response to cytokine / positive regulation of interleukin-8 production / response to ischemia / negative regulation of protein catabolic process / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 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 | 6nv2.cif.gz | 157.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nv2.ent.gz | 124.5 KB | Display | PDB format |
PDBx/mmJSON format | 6nv2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nv2_validation.pdf.gz | 789.4 KB | Display | wwPDB validaton report |
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Full document | 6nv2_full_validation.pdf.gz | 791.3 KB | Display | |
Data in XML | 6nv2_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 6nv2_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/6nv2 ftp://data.pdbj.org/pub/pdb/validation_reports/nv/6nv2 | HTTPS FTP |
-Related structure data
Related structure data | 6qhlC 6qhmC 3mhrS C: citing same article (ref.) S: Starting model for refinement |
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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-CL / |
#4: Sugar | ChemComp-0V4 / ( |
#5: 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: 2.57 Å3/Da / Density % sol: 52.17 % |
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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: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 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: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→45.47 Å / Num. obs: 352244 / % possible obs: 98.9 % / Redundancy: 3.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.029 / Rrim(I) all: 0.054 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.13→1.15 Å / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 4.4 / CC1/2: 0.929 / Rrim(I) all: 0.258 / % possible all: 99.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MHR Resolution: 1.13→45.468 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.51
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.13→45.468 Å
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Refine LS restraints |
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LS refinement shell |
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