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- PDB-5oma: CH3 chimera of human 14-3-3 sigma with the StARD1 peptide includi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5oma | ||||||||||||
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Title | CH3 chimera of human 14-3-3 sigma with the StARD1 peptide including Ser57 | ||||||||||||
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![]() | SIGNALING PROTEIN / 14-3-3 proteins / Protein chimera / phosphopeptide-binding | ||||||||||||
Function / homology | ![]() positive regulation of bile acid biosynthetic process / cellular lipid metabolic process / regulation of steroid biosynthetic process / intracellular cholesterol transport / glucocorticoid metabolic process / Pregnenolone biosynthesis / steroid biosynthetic process / cholesterol transfer activity / cholesterol binding / regulation of epidermal cell division ...positive regulation of bile acid biosynthetic process / cellular lipid metabolic process / regulation of steroid biosynthetic process / intracellular cholesterol transport / glucocorticoid metabolic process / Pregnenolone biosynthesis / steroid biosynthetic process / cholesterol transfer activity / cholesterol binding / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / Mitochondrial protein degradation / protein sequestering activity / protein kinase A signaling / negative regulation of innate immune response / protein export from nucleus / cholesterol metabolic process / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / mitochondrial intermembrane space / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / positive regulation of cell growth / regulation of cell cycle / mitochondrial matrix / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Sluchanko, N.N. / Tugaeva, K.V. / Greive, S.J. / Antson, A.A. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Chimeric 14-3-3 proteins for unraveling interactions with intrinsically disordered partners. Authors: Sluchanko, N.N. / Tugaeva, K.V. / Greive, S.J. / Antson, A.A. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 375.6 KB | Display | ![]() |
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PDB format | ![]() | 313.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ok9C ![]() 5okfC ![]() 5om0C ![]() 5lu1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 5 molecules ABCDH
#1: Protein | Mass: 27835.160 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: residues 75-77 were replaced by alanines to reduce surface entropy and improve crystallization Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | | Mass: 358.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Used to model a piece of the disordered peptide fused to the 14-3-3 protein core, of undetermined sequence. Most likely correspond to a continuation of chain D'. Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 4 molecules ![](data/chem/img/TRS.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-TRS / |
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#4: Chemical | ChemComp-PO4 / |
#5: Chemical | ChemComp-SO4 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M bis-Trispropane pH 6.5, 0.2 M ammonium sulfate, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 20, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.89→47 Å / Num. obs: 12047 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 12.71 % / Biso Wilson estimate: 136.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.265 / Rrim(I) all: 0.277 / Χ2: 0.902 / Net I/σ(I): 6.88 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LU1 (monomer) Resolution: 3.9→47 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.964 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.751
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Displacement parameters | Biso max: 300 Å2 / Biso mean: 198.79 Å2 / Biso min: 86.62 Å2
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Refine analyze | Luzzati coordinate error obs: 0.59 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.9→47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.9→4.27 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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