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Yorodumi- PDB-6mib: Crystal structure of the ILK ATP-binding deficient mutant (L207W)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mib | ||||||
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Title | Crystal structure of the ILK ATP-binding deficient mutant (L207W)/alpha-parvin core complex | ||||||
Components |
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Keywords | CELL ADHESION / Pseudokinase / Protein complex | ||||||
Function / homology | Function and homology information actin-mediated cell contraction / smooth muscle cell chemotaxis / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / negative regulation of neural precursor cell proliferation / positive regulation of signal transduction / nerve development / Cell-extracellular matrix interactions / myelination in peripheral nervous system / fibroblast migration ...actin-mediated cell contraction / smooth muscle cell chemotaxis / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / negative regulation of neural precursor cell proliferation / positive regulation of signal transduction / nerve development / Cell-extracellular matrix interactions / myelination in peripheral nervous system / fibroblast migration / cell projection organization / outflow tract septum morphogenesis / positive regulation of BMP signaling pathway / neural precursor cell proliferation / establishment or maintenance of epithelial cell apical/basal polarity / heterotypic cell-cell adhesion / sprouting angiogenesis / establishment or maintenance of cell polarity / branching involved in ureteric bud morphogenesis / protein kinase inhibitor activity / outflow tract morphogenesis / cilium assembly / positive regulation of osteoblast differentiation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of phosphorylation / tumor necrosis factor-mediated signaling pathway / sarcomere / substrate adhesion-dependent cell spreading / cell-matrix adhesion / phosphatidylinositol 3-kinase/protein kinase B signal transduction / integrin-mediated signaling pathway / cell morphogenesis / platelet aggregation / Z disc / positive regulation of canonical Wnt signaling pathway / actin cytoskeleton / lamellipodium / actin binding / regulation of cell shape / actin cytoskeleton organization / positive regulation of canonical NF-kappaB signal transduction / protein stabilization / non-specific serine/threonine protein kinase / cadherin binding / positive regulation of protein phosphorylation / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / protein kinase binding / positive regulation of DNA-templated transcription / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Fukuda, K. / Qin, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Non-catalytic signaling by pseudokinase ILK for regulating cell adhesion. Authors: Vaynberg, J. / Fukuda, K. / Lu, F. / Bialkowska, K. / Chen, Y. / Plow, E.F. / Qin, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mib.cif.gz | 97.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mib.ent.gz | 72.2 KB | Display | PDB format |
PDBx/mmJSON format | 6mib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/6mib ftp://data.pdbj.org/pub/pdb/validation_reports/mi/6mib | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31045.064 Da / Num. of mol.: 1 / Mutation: L207W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ILK, ILK1, ILK2 / Production host: Escherichia coli (E. coli) References: UniProt: Q13418, non-specific serine/threonine protein kinase |
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#2: Protein | Mass: 14843.072 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARVA, MXRA2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NVD7 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.49 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 16% PEG 3,350, 0.1 M Bis-Tris Propane, pH 7.4, 5% 1-Propanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 39797 / % possible obs: 98.9 % / Redundancy: 4.6 % / Net I/σ(I): 41.78 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 7.69 / Num. unique obs: 1954 / % possible all: 95.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20.88 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.186 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.115 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.898 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→20.88 Å
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