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- PDB-7obh: Crystal structure of 14-3-3 sigma in complex with NPM1 phosphopep... -
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Basic information
Entry | Database: PDB / ID: 7obh | ||||||
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Title | Crystal structure of 14-3-3 sigma in complex with NPM1 phosphopeptide and stabilizer Fusicoccin-A | ||||||
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![]() | SIGNALING PROTEIN / 14-3-3 sigma protein-peptide-Stabilizer complex | ||||||
Function / homology | ![]() regulation of eIF2 alpha phosphorylation by dsRNA / regulation of mRNA stability involved in cellular response to UV / regulation of endoribonuclease activity / negative regulation of centrosome duplication / regulation of endodeoxyribonuclease activity / positive regulation of cell cycle G2/M phase transition / regulation of centriole replication / granular component / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / negative regulation of protein kinase activity by regulation of protein phosphorylation ...regulation of eIF2 alpha phosphorylation by dsRNA / regulation of mRNA stability involved in cellular response to UV / regulation of endoribonuclease activity / negative regulation of centrosome duplication / regulation of endodeoxyribonuclease activity / positive regulation of cell cycle G2/M phase transition / regulation of centriole replication / granular component / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / negative regulation of protein kinase activity by regulation of protein phosphorylation / SARS-CoV-1-host interactions / Tat protein binding / regulation of centrosome duplication / ALK mutants bind TKIs / spindle pole centrosome / Nuclear import of Rev protein / centrosome cycle / nucleocytoplasmic transport / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / protein kinase inhibitor activity / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / ribosomal large subunit binding / Regulation of localization of FOXO transcription factors / ribosomal small subunit binding / keratinocyte proliferation / NF-kappaB binding / ribosomal large subunit export from nucleus / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / ribosomal small subunit export from nucleus / Nuclear events stimulated by ALK signaling in cancer / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / ribosomal subunit export from nucleus / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / core promoter sequence-specific DNA binding / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / Deposition of new CENPA-containing nucleosomes at the centromere / protein kinase A signaling / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / ribosome assembly / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / SUMOylation of transcription cofactors / ribosomal large subunit biogenesis / stem cell proliferation / positive regulation of translation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein-DNA complex / TP53 Regulates Metabolic Genes / intracellular protein transport / negative regulation of protein kinase activity / PKR-mediated signaling / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein localization / cellular response to UV / : / intrinsic apoptotic signaling pathway in response to DNA damage / cellular senescence / unfolded protein binding / Signaling by ALK fusions and activated point mutants / nucleosome assembly / ribosomal small subunit biogenesis / positive regulation of NF-kappaB transcription factor activity / histone binding / positive regulation of cell growth / DNA-binding transcription factor binding / transcription coactivator activity / rRNA binding / regulation of cell cycle / chromatin remodeling / ribonucleoprotein complex / cadherin binding / negative regulation of cell population proliferation / DNA repair / focal adhesion / centrosome / chromatin binding / positive regulation of cell population proliferation / nucleolus / negative regulation of apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / extracellular space Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Centorrino, F. / Andlovic, B. / Ottmann, C. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: IFN alpha primes cancer cells for Fusicoccin-induced cell death via 14-3-3 PPI stabilization. Authors: Andlovic, B. / Heilmann, G. / Ninck, S. / Andrei, S.A. / Centorrino, F. / Higuchi, Y. / Kato, N. / Brunsveld, L. / Arkin, M. / Menninger, S. / Choidas, A. / Wolf, A. / Klebl, B. / Kaschani, ...Authors: Andlovic, B. / Heilmann, G. / Ninck, S. / Andrei, S.A. / Centorrino, F. / Higuchi, Y. / Kato, N. / Brunsveld, L. / Arkin, M. / Menninger, S. / Choidas, A. / Wolf, A. / Klebl, B. / Kaschani, F. / Kaiser, M. / Eickhoff, J. / 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 | ![]() | 139.3 KB | Display | ![]() |
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PDB format | ![]() | 87.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 855 KB | Display | ![]() |
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Full document | ![]() | 857.4 KB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ob5C ![]() 7ob8C ![]() 7obcC ![]() 7obdC ![]() 7obgC ![]() 7obkC ![]() 7oblC ![]() 7obsC ![]() 7obtC ![]() 7obxC ![]() 7obyC ![]() 4jc3S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
#1: Protein | Mass: 28226.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1554.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Chemical | ChemComp-FSC / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.47 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.095 M Hepes pH 7.3, 25%PEG 400, 0.19 M CaCl2 and 5 % Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5419 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Sep 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 2→33.23 Å / Num. obs: 19953 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 7.52 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.101 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2→2.04 Å / Redundancy: 6 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 6.6 / Num. unique obs: 979 / CC1/2: 0.952 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JC3 Resolution: 2→33.23 Å / SU ML: 0.162 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.1015 / Stereochemistry target values: GeoStd + Monomer Library
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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 mean: 11.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→33.23 Å
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Refine LS restraints |
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LS refinement shell |
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