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- PDB-5xq0: Structural basis of kindlin-mediated integrin recognition and act... -
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Basic information
Entry | Database: PDB / ID: 5xq0 | ||||||
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Title | Structural basis of kindlin-mediated integrin recognition and activation | ||||||
![]() | Fermitin family homolog 2,Integrin beta-1 | ||||||
![]() | SIGNALING PROTEIN / Integrin Binding / Multi-domain containing protein | ||||||
Function / homology | ![]() Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Laminin interactions / MET interacts with TNS proteins / Elastic fibre formation / Cell-extracellular matrix interactions / Fibronectin matrix formation / Syndecan interactions / C-X3-C chemokine binding / Signal transduction by L1 / Molecules associated with elastic fibres ...Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Laminin interactions / MET interacts with TNS proteins / Elastic fibre formation / Cell-extracellular matrix interactions / Fibronectin matrix formation / Syndecan interactions / C-X3-C chemokine binding / Signal transduction by L1 / Molecules associated with elastic fibres / MET activates PTK2 signaling / TGF-beta receptor signaling activates SMADs / Basigin interactions / RAC3 GTPase cycle / ECM proteoglycans / RAC2 GTPase cycle / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha6-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / positive regulation of glutamate uptake involved in transmission of nerve impulse / myoblast fate specification / integrin alpha9-beta1 complex / adherens junction maintenance / regulation of collagen catabolic process / cardiac cell fate specification / integrin binding involved in cell-matrix adhesion / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / reactive gliosis / protein localization to cell junction / RAC1 GTPase cycle / formation of radial glial scaffolds / cerebellar climbing fiber to Purkinje cell synapse / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / positive regulation of wound healing, spreading of epidermal cells / myelin sheath abaxonal region / Integrin cell surface interactions / positive regulation of mesenchymal stem cell proliferation / Cell surface interactions at the vascular wall / CD40 signaling pathway / calcium-independent cell-matrix adhesion / positive regulation of fibroblast growth factor receptor signaling pathway / GPER1 signaling / RHOG GTPase cycle / integrin alphav-beta1 complex / regulation of synapse pruning / basement membrane organization / cardiac muscle cell myoblast differentiation / positive regulation of integrin activation / fibroblast migration / leukocyte tethering or rolling / cardiac muscle cell differentiation / germ cell migration / type I transforming growth factor beta receptor binding / integrin activation / focal adhesion assembly / myoblast fusion / positive regulation of vascular endothelial growth factor signaling pathway / mesodermal cell differentiation / negative regulation of vascular permeability / myoblast differentiation / cell migration involved in sprouting angiogenesis / axon extension / protein localization to membrane / I band / central nervous system neuron differentiation / limb development / cardiac muscle tissue development / heterotypic cell-cell adhesion / positive regulation of fibroblast migration / regulation of spontaneous synaptic transmission / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sarcomere organization / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / muscle organ development / positive regulation of wound healing / dendrite morphogenesis / positive regulation of neuroblast proliferation / negative regulation of neuron differentiation / negative regulation of fat cell differentiation / negative regulation of Rho protein signal transduction / positive regulation of Rho protein signal transduction / SMAD binding / response to muscle activity / phosphatidylinositol-3,4,5-trisphosphate binding / establishment of mitotic spindle orientation / lamellipodium membrane / fibronectin binding / negative regulation of anoikis / cellular response to low-density lipoprotein particle stimulus / intercalated disc / positive regulation of focal adhesion assembly Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, H. / Yang, H. / Sun, K. / Zhang, Z. / Yu, C. / Wei, Z. | ||||||
![]() | ![]() 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 | ![]() | 353.1 KB | Display | ![]() |
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PDB format | ![]() | 285.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 489.5 KB | Display | ![]() |
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Full document | ![]() | 499.2 KB | Display | |
Data in XML | ![]() | 29.4 KB | Display | |
Data in CIF | ![]() | 39.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xpyC ![]() 5xpzSC ![]() 5xq1C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 56066.676 Da / Num. of mol.: 2 / Fragment: UNP residues 784-798 / Mutation: 168-217 deletion, 337-512 deletion Source method: isolated from a genetically manipulated source Details: Beta-integrin tail sequence was fused to the C-terminus of kindlin2 Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.79 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M potassium chloride, 0.05 M HEPES pH 7.5, 35% v/v pentaerythritol propoxylate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 22, 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: 2.75→50 Å / Num. obs: 34443 / % possible obs: 98.7 % / Redundancy: 4 % / Biso Wilson estimate: 67.25 Å2 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.045 / Rrim(I) all: 0.098 / Χ2: 2.621 / Net I/σ(I): 12 / Num. measured all: 139053 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XPZ Resolution: 2.75→45.858 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 207.14 Å2 / Biso mean: 74.5935 Å2 / Biso min: 27.57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.75→45.858 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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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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