+Open data
-Basic information
Entry | Database: PDB / ID: 3kmu | ||||||
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Title | Crystal structure of the ILK/alpha-parvin core complex (apo) | ||||||
Components |
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Keywords | CELL ADHESION / ANK repeat / ATP-binding / Cell junction / Cell membrane / Integrin-binding protein / Membrane / Nucleotide-binding / Phosphoprotein / pseudokinase / Actin-binding / Alternative splicing | ||||||
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 / neural precursor cell proliferation / positive regulation of BMP signaling pathway / 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 / cell-matrix adhesion / sarcomere / substrate adhesion-dependent cell spreading / 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 / MAD / Resolution: 1.8 Å | ||||||
Authors | Fukuda, K. / Qin, J. | ||||||
Citation | Journal: Mol.Cell / Year: 2009 Title: The pseudoactive site of ILK is essential for its binding to alpha-Parvin and localization to focal adhesions. Authors: Fukuda, K. / Gupta, S. / Chen, K. / Wu, C. / Qin, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kmu.cif.gz | 94.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kmu.ent.gz | 76.1 KB | Display | PDB format |
PDBx/mmJSON format | 3kmu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/3kmu ftp://data.pdbj.org/pub/pdb/validation_reports/km/3kmu | 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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Details | The heterodimeric complex observed in the asymmetric unit is relevant to the biological assembly unit in vivo. |
-Components
#1: Protein | Mass: 31675.428 Da / Num. of mol.: 1 Fragment: C-terminal pseudokinase domain: UNP residues 183-452 Mutation: C346S, C422S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ILK, ILK1, ILK2 / Plasmid: pST39 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q13418 |
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#2: Protein | Mass: 14983.758 Da / Num. of mol.: 1 Fragment: C-terminal calponin homology domain: UNP residues 248-372 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARVA, MXRA2 / Plasmid: pST39 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / 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: 2.6 Å3/Da / Density % sol: 52.61 % |
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Crystal grow | Temperature: 277 K / pH: 6.8 Details: 0.05 M Bis-Tris, 12% PEG 5000 MME, 5% 1-Propyl alcohol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97880, 0.97900 | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 30, 2008 | |||||||||
Radiation | Monochromator: SI(111) DOUBLE-CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.75→58.82 Å / Num. obs: 94370 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.058 / Net I/σ(I): 28.2 | |||||||||
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.44 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→58.82 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.642 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: THE FRIEDEL PAIRS WERE USED IN PHASING
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→58.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å / Total num. of bins used: 20
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