[English] 日本語
![](img/lk-miru.gif)
- PDB-7oqw: Ternary complex of 14-3-3 sigma, Amot-p130 phosphopeptide, and WQ178 -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7oqw | ||||||
---|---|---|---|---|---|---|---|
Title | Ternary complex of 14-3-3 sigma, Amot-p130 phosphopeptide, and WQ178 | ||||||
![]() |
| ||||||
![]() | SIGNALING PROTEIN / protein-peptide complex small-molecule | ||||||
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
| ||||||
![]() | ![]() Title: A crystallography-based study of fragment extensions into the 14-3-3 binding groove Authors: Centorrino, F. / Wu, Q. / Cossar, P. / Brunsveld, L. / Ottmann, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 129.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 81.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 994.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 995.9 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 19.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7opwC ![]() 7oq7C ![]() 7oq8C ![]() 7oq9C ![]() 7oqaC ![]() 7oqgC ![]() 7oqjC ![]() 7oqsC ![]() 7oquC ![]() 7or3C ![]() 7or5C ![]() 7or7C ![]() 7or8C ![]() 7orgC ![]() 7orhC ![]() 7orsC ![]() 7ortC ![]() 4jc3S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#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.) ![]() | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.45 % |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 0.095 M Hepes pH7.5, 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: Feb 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→41.41 Å / Num. obs: 22109 / % possible obs: 97.2 % / Redundancy: 6.4 % / Biso Wilson estimate: 14.88 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.052 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 6 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1550 / CC1/2: 0.65 / Rpim(I) all: 0.224 / % possible all: 94.4 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4jc3 Resolution: 1.9→41.41 Å / SU ML: 0.1843 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 21.0921 / 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: 21.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→41.41 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|