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- PDB-5xpy: Structural basis of kindlin-mediated integrin recognition and act... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xpy | |||||||||
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Title | Structural basis of kindlin-mediated integrin recognition and activation | |||||||||
![]() | Fermitin family homolog 2 | |||||||||
![]() | SIGNALING PROTEIN / Integrin Binding / Multi-domain containing protein | |||||||||
Function / homology | ![]() Cell-extracellular matrix interactions / RAC3 GTPase cycle / adherens junction maintenance / RAC1 GTPase cycle / protein localization to cell junction / positive regulation of wound healing, spreading of epidermal cells / positive regulation of mesenchymal stem cell proliferation / positive regulation of integrin activation / type I transforming growth factor beta receptor binding / integrin activation ...Cell-extracellular matrix interactions / RAC3 GTPase cycle / adherens junction maintenance / RAC1 GTPase cycle / protein localization to cell junction / positive regulation of wound healing, spreading of epidermal cells / positive regulation of mesenchymal stem cell proliferation / positive regulation of integrin activation / type I transforming growth factor beta receptor binding / integrin activation / protein localization to membrane / focal adhesion assembly / negative regulation of vascular permeability / I band / limb development / negative regulation of fat cell differentiation / SMAD binding / positive regulation of focal adhesion assembly / phosphatidylinositol-3,4,5-trisphosphate binding / lamellipodium membrane / positive regulation of osteoblast differentiation / positive regulation of epithelial to mesenchymal transition / stress fiber / positive regulation of substrate adhesion-dependent cell spreading / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of stress fiber assembly / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / cell-matrix adhesion / integrin-mediated signaling pathway / adherens junction / cytoplasmic side of plasma membrane / Wnt signaling pathway / positive regulation of protein localization to nucleus / actin filament binding / integrin binding / cell cortex / regulation of cell shape / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / focal adhesion / protein kinase binding / cell surface / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Li, H. / Yang, H. / Sun, K. / Zhang, Z. / Yu, C. / Wei, Z. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of kindlin-mediated integrin recognition and activation Authors: Li, H. / Deng, Y. / Sun, K. / Yang, H. / Liu, J. / Wang, M. / Zhang, Z. / Lin, J. / Wu, C. / Wei, Z. / Yu, 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 | ![]() | 205.5 KB | Display | ![]() |
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PDB format | ![]() | 162.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.2 KB | Display | ![]() |
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Full document | ![]() | 461.1 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 26.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xpzSC ![]() 5xq0C ![]() 5xq1C 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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Unit cell |
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Components
#1: Protein | Mass: 55083.320 Da / Num. of mol.: 1 / Fragment: UNP residues 15-680 / Mutation: 168-217 deletion, 367-512 deletion Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.4 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 4.0 M Ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.099→31.408 Å / Num. obs: 42158 / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.043 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.761 / Rsym value: 0.761 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XPZ Resolution: 2.099→31.408 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.22 / Stereochemistry target values: ML Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.099→31.408 Å
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Refine LS restraints |
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LS refinement shell |
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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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