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Yorodumi- PDB-1zvz: Vinculin Head (0-258) in Complex with the Talin Rod Residue 820-844 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zvz | ||||||
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Title | Vinculin Head (0-258) in Complex with the Talin Rod Residue 820-844 | ||||||
Components |
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Keywords | PROTEIN BINDING / talin / vinculin / complex | ||||||
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 / vinculin binding / muscle alpha-actinin binding / MAP2K and MAPK activation / alpha-catenin binding / fascia adherens / cell-cell contact zone / costamere / apical junction assembly / regulation of establishment of endothelial barrier / adherens junction assembly / 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 / ruffle / cell projection / Neutrophil degranulation / morphogenesis of an epithelium / adherens junction / sarcolemma / neuromuscular junction / structural constituent of cytoskeleton / cell-cell adhesion / ruffle membrane / Z disc / beta-catenin binding / actin filament binding / cell-cell junction / actin cytoskeleton / integrin binding / scaffold protein binding / mitochondrial inner membrane / cytoskeleton / cell adhesion / cadherin binding / focal adhesion / ubiquitin protein ligase binding / structural molecule activity / cell surface / protein homodimerization activity / protein-containing complex / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Gingras, A.R. / Ziegler, W.H. / Barsukov, I.L. / Roberts, G.C. / Critchley, D.R. / Emsley, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Mapping and consensus sequence identification for multiple vinculin binding sites within the talin rod Authors: Gingras, A.R. / Ziegler, W.H. / Frank, R. / Barsukov, I.L. / Roberts, G.C. / Critchley, D.R. / Emsley, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zvz.cif.gz | 71.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zvz.ent.gz | 51.6 KB | Display | PDB format |
PDBx/mmJSON format | 1zvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/1zvz ftp://data.pdbj.org/pub/pdb/validation_reports/zv/1zvz | HTTPS FTP |
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-Related structure data
Related structure data | 1zw2C 1zw3C 1xwjS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 31195.908 Da / Num. of mol.: 1 / Fragment: Residues 0-258 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: VCL, VINC1 / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P12003 |
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#2: Protein/peptide | Mass: 2645.021 Da / Num. of mol.: 1 / Fragment: Residues 820-844 / Source method: obtained synthetically Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN GALLUS GALLUS(CHICKEN). References: UniProt: P54939 |
#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: 2.1 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 13, 2005 / Details: TOROIDAL ZERODUR MIRROR |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 27873 / % possible obs: 97.7 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.09 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XWJ Resolution: 1.8→26.29 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.895 / SU B: 6.398 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.204 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→26.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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