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Yorodumi- PDB-1tr2: Crystal structure of human full-length vinculin (residues 1-1066) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tr2 | ||||||
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Title | Crystal structure of human full-length vinculin (residues 1-1066) | ||||||
Components | VINCULIN ISOFORM 1 | ||||||
Keywords | CELL ADHESION / ACTIN-BINDING | ||||||
Function / homology | Function and homology information regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / cell-substrate junction / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding ...regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / cell-substrate junction / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / 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 / maintenance of blood-brain barrier / regulation of focal adhesion assembly / brush border / Signaling by ALK fusions and activated point mutants / Smooth Muscle Contraction / cell-matrix adhesion / negative regulation of cell migration / cell projection / morphogenesis of an epithelium / adherens junction / sarcolemma / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet aggregation / beta-catenin binding / specific granule lumen / extracellular vesicle / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cell-cell junction / Signaling by BRAF and RAF1 fusions / Platelet degranulation / actin binding / secretory granule lumen / ficolin-1-rich granule lumen / molecular adaptor activity / cytoskeleton / cell adhesion / cadherin binding / membrane raft / focal adhesion / ubiquitin protein ligase binding / Neutrophil degranulation / structural molecule activity / protein-containing complex / extracellular exosome / extracellular region / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å | ||||||
Authors | Borgon, R.A. / Vonrhein, C. / Bricogne, G. / Bois, P.R. / Izard, T. | ||||||
Citation | Journal: Structure / Year: 2004 Title: Crystal Structure of Human Vinculin Authors: Borgon, R.A. / Vonrhein, C. / Bricogne, G. / Bois, P.R. / Izard, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tr2.cif.gz | 403.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tr2.ent.gz | 340.3 KB | Display | PDB format |
PDBx/mmJSON format | 1tr2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/1tr2 ftp://data.pdbj.org/pub/pdb/validation_reports/tr/1tr2 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 118563.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VCL / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) and BL21(DE3) / References: UniProt: P18206 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 11 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.97 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97927 |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97927 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→56.86 Å / Num. obs: 48752 / % possible obs: 100 % / Redundancy: 23.7 % / Biso Wilson estimate: 103.211 Å2 / Rmerge(I) obs: 0.154 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.9→2.98 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 1.4 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.9→56.86 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: SOME OF THE WATER MOLECULES ARE PLACED IN DISORDERED DENSITY.
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Displacement parameters | Biso mean: 92.83 Å2
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Refine analyze | Luzzati coordinate error obs: 0.4897 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→56.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.07 Å / Total num. of bins used: 9
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