[English] 日本語
![](img/lk-miru.gif)
- PDB-7nn2: Crystal structure of 14-3-3 sigma in complex with 13mer Amot-p130... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7nn2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of 14-3-3 sigma in complex with 13mer Amot-p130 peptide and fragment 41 | ||||||
![]() |
| ||||||
![]() | 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 / endocytic vesicle / keratinocyte proliferation / positive regulation of cell size / 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 / negative regulation of angiogenesis / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / stress fiber / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / ruffle / protein sequestering activity / protein kinase A signaling / negative regulation of innate immune response / protein export from nucleus / regulation of cell migration / 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 / actin filament / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / chemotaxis / intrinsic apoptotic signaling pathway in response to DNA damage / cell junction / protein localization / lamellipodium / signaling receptor activity / positive regulation of cell growth / actin cytoskeleton organization / cytoplasmic vesicle / 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
| ||||||
![]() | ![]() Title: Fragment-based exploration of the 14-3-3/Amot-p130 interface. Authors: Centorrino, F. / Andlovic, B. / Cossar, P. / Brunsveld, L. / Ottmann, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 135.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 85.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7nmaC ![]() 7nmwC ![]() 7nmxC ![]() 7nndC ![]() 7nneC ![]() 7np2C ![]() 7npbC ![]() 7npgC ![]() 4jc3S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
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.) ![]() ![]() ![]() |
---|---|
#2: Protein/peptide | Mass: 1626.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 4 types, 381 molecules ![](data/chem/img/K8W.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-K8W / |
---|---|
#4: Chemical | ChemComp-CA / |
#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.49 % |
---|---|
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 |
---|---|
Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5419 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→41.16 Å / Num. obs: 26830 / % possible obs: 98.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 10.83 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.038 / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 1.8→1.85 Å / Rmerge(I) obs: 0.103 / Mean I/σ(I) obs: 13.3 / Num. unique obs: 1844 / CC1/2: 0.993 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4JC3 Resolution: 1.8→34.45 Å / SU ML: 0.138 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.119 / Stereochemistry target values: GeoStd + Monomer Library
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→34.45 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|