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Yorodumi- PDB-1qkr: Crystal structure of the vinculin tail and a pathway for activation -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qkr | ||||||
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Title | Crystal structure of the vinculin tail and a pathway for activation | ||||||
Components | VINCULIN | ||||||
Keywords | ACTIN CYTOSKELETON / CELL ADHESION / HELICAL BUNDLE / LIPID BINDING | ||||||
Function / homology | Function and homology information muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / epithelial cell-cell adhesion / zonula adherens ...muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / muscle alpha-actinin binding / MAP2K and MAPK activation / alpha-catenin binding / vinculin binding / fascia adherens / cell-cell contact zone / adherens junction assembly / apical junction assembly / costamere / regulation of establishment of endothelial barrier / axon extension / protein localization to cell surface / lamellipodium assembly / regulation of focal adhesion assembly / alpha-actinin binding / brush border / skeletal muscle myofibril / stress fiber / regulation of cell migration / Neutrophil degranulation / cell projection / morphogenesis of an epithelium / adherens junction / neuromuscular junction / sarcolemma / beta-catenin binding / Z disc / cell-cell junction / actin filament binding / actin cytoskeleton / scaffold protein binding / mitochondrial inner membrane / cytoskeleton / cell adhesion / cadherin binding / focal adhesion / ubiquitin protein ligase binding / structural molecule activity / protein homodimerization activity / protein-containing complex / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | GALLUS GALLUS (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å | ||||||
Authors | Bakolitsa, C. / De Pereda, J.M. / Bagshaw, C.R. / Critchley, D.R. / Liddington, R.C. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1999 Title: Crystal Structure of the Vinculin Tail and a Pathway for Activation Authors: Bakolitsa, C. / De Pereda, J.M. / Bagshaw, C.R. / Critchley, D.R. / Liddington, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qkr.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qkr.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 1qkr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qkr_validation.pdf.gz | 447.5 KB | Display | wwPDB validaton report |
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Full document | 1qkr_full_validation.pdf.gz | 453.3 KB | Display | |
Data in XML | 1qkr_validation.xml.gz | 19 KB | Display | |
Data in CIF | 1qkr_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/1qkr ftp://data.pdbj.org/pub/pdb/validation_reports/qk/1qkr | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21629.486 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) GALLUS GALLUS (chicken) / Tissue: MUSCLE / Gene: VCL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12003 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 Details: 25% (W/V) PEG 2000, 0.2 M (NH4)2SO4, 0.1 M CH3COO PH 5.0 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 44 % | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 8 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→10 Å / Num. obs: 30415 / % possible obs: 95.5 % / Redundancy: 2.6 % / Biso Wilson estimate: 18.4 Å2 / Rsym value: 0.064 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.8→1.91 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.27 / % possible all: 88.3 |
Reflection | *PLUS Lowest resolution: 25 Å / % possible obs: 98.6 % / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.8→10 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 70.2752 Å2 / ksol: 0.426906 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.28 |