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- PDB-8c30: Crystal structure of 14-3-3 in complex with PyrinpS242 and a prot... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8c30 | ||||||
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Title | Crystal structure of 14-3-3 in complex with PyrinpS242 and a protein/peptide interface fragment | ||||||
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![]() | PROTEIN BINDING / protein-peptide interaction / phosphorylation reader protein / immunology / scaffolding / intrinsic disorder motif | ||||||
Function / homology | ![]() pyroptosome complex assembly / negative regulation of macrophage inflammatory protein 1 alpha production / regulation of interleukin-1 beta production / canonical inflammasome complex / negative regulation of NLRP3 inflammasome complex assembly / negative regulation of interleukin-12 production / positive regulation of cysteine-type endopeptidase activity / pattern recognition receptor signaling pathway / microtubule associated complex / negative regulation of interleukin-1 beta production ...pyroptosome complex assembly / negative regulation of macrophage inflammatory protein 1 alpha production / regulation of interleukin-1 beta production / canonical inflammasome complex / negative regulation of NLRP3 inflammasome complex assembly / negative regulation of interleukin-12 production / positive regulation of cysteine-type endopeptidase activity / pattern recognition receptor signaling pathway / microtubule associated complex / negative regulation of interleukin-1 beta production / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / pyroptotic inflammatory response / response to type II interferon / The NLRP3 inflammasome / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of cytokine production involved in inflammatory response / autophagosome / negative regulation of keratinocyte proliferation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / positive regulation of autophagy / 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 / ruffle / protein kinase A signaling / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / positive regulation of interleukin-1 beta production / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of inflammatory response / positive regulation of inflammatory response / intrinsic apoptotic signaling pathway in response to DNA damage / ubiquitin protein ligase activity / lamellipodium / actin binding / cytoplasmic vesicle / positive regulation of cell growth / regulation of gene expression / microtubule / regulation of cell cycle / protein ubiquitination / cadherin binding / inflammatory response / innate immune response / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / zinc ion binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lau, R. / Ottmann, C. | ||||||
Funding support | 1items
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![]() | ![]() Title: 14-3-3/Pyrin complex Authors: Ottmann, C. / Lau, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 520.8 KB | Display | ![]() |
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Full document | ![]() | 524.3 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8c28C ![]() 8c2yC 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
-Protein / Protein/peptide , 2 types, 2 molecules AAAPPP
#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: 1499.692 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 5 types, 214 molecules ![](data/chem/img/463.gif)
![](data/chem/img/PE5.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PE5.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-463 / |
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#4: Chemical | ChemComp-PE5 / |
#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-CA / |
#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: 2.56 Å3/Da / Density % sol: 51.95 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.19 M CaCl 2 , 5% glycerol, 26% PEG 400, 0.095 M HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033215 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→62.48 Å / Num. obs: 55917 / % possible obs: 98.1 % / Redundancy: 6.4 % / CC1/2: 0.998 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.4→1.44 Å / Num. unique obs: 3331 / CC1/2: 0.948 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: in house Resolution: 1.4→45.488 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.213 / WRfactor Rwork: 0.187 / SU B: 0.808 / SU ML: 0.033 / Average fsc free: 0.9473 / Average fsc work: 0.9548 / Cross valid method: FREE R-VALUE / ESU R: 0.058 / ESU R Free: 0.06 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.007 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→45.488 Å
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Refine LS restraints |
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LS refinement shell |
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