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- PDB-7nnd: Crystal structure of 14-3-3 sigma in complex with 13mer Amot-p130... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7nnd | ||||||
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Title | Crystal structure of 14-3-3 sigma in complex with 13mer Amot-p130 peptide and fragment 09 | ||||||
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![]() | SIGNALING PROTEIN / protein-peptide complex fragment soaking | ||||||
Function / homology | ![]() establishment of cell polarity involved in ameboidal cell migration / cell migration involved in gastrulation / positive regulation of embryonic development / Regulation of CDH11 function / blood vessel endothelial cell migration / establishment of epithelial cell polarity / angiostatin binding / hippo signaling / gastrulation with mouth forming second / negative regulation of vascular permeability ...establishment of cell polarity involved in ameboidal cell migration / cell migration involved in gastrulation / positive regulation of embryonic development / Regulation of CDH11 function / blood vessel endothelial cell migration / establishment of epithelial cell polarity / angiostatin binding / hippo signaling / gastrulation with mouth forming second / negative regulation of vascular permeability / Signaling by Hippo / cell-cell junction assembly / regulation of small GTPase mediated signal transduction / 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 / positive regulation of cell size / keratinocyte proliferation / endocytic vesicle / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / bicellular tight junction / negative regulation of keratinocyte proliferation / positive regulation of blood vessel endothelial cell migration / vasculogenesis / 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 / stress fiber / RHO GTPases activate PKNs / regulation of cell migration / positive regulation of stress fiber assembly / ruffle / protein kinase A signaling / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / negative regulation of angiogenesis / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein localization / intrinsic apoptotic signaling pathway in response to DNA damage / chemotaxis / cell junction / lamellipodium / signaling receptor activity / cytoplasmic vesicle / actin cytoskeleton organization / positive regulation of cell growth / angiogenesis / in utero embryonic development / regulation of cell cycle / cadherin binding / external side of plasma membrane / protein kinase binding / negative regulation of transcription by RNA polymerase II / cell surface / signal transduction / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Centorrino, F. / Ottmann, C. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: Fragment-based exploration of the 14-3-3/Amot-p130 interface. Authors: Centorrino, F. / Andlovic, B. / Cossar, P. / Brunsveld, L. / 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 | ![]() | 137.7 KB | Display | ![]() |
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PDB format | ![]() | 87.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 789.2 KB | Display | ![]() |
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Full document | ![]() | 789.1 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 22.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nmaC ![]() 7nmwC ![]() 7nmxC ![]() 7nn2C ![]() 7nneC ![]() 7np2C ![]() 7npbC ![]() 7npgC ![]() 4jc3S 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AP
#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: 1626.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 4 types, 360 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K7N.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K7N.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CL / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-K7N / |
#6: 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: 2.43 Å3/Da / Density % sol: 49.43 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 0.095 M Hepes pH 7.5, 26% 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→62.72 Å / Num. obs: 55890 / % possible obs: 98.7 % / Redundancy: 4 % / Biso Wilson estimate: 13.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.4→1.44 Å / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 4058 / CC1/2: 0.915 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JC3 Resolution: 1.4→45.46 Å / SU ML: 0.0952 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.043 / 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: 19.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→45.46 Å
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Refine LS restraints |
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LS refinement shell |
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