+Open data
-Basic information
Entry | Database: PDB / ID: 5l0d | ||||||
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Title | Human Metavinculin(residues 959-1130) in complex with PIP2 | ||||||
Components | Vinculin | ||||||
Keywords | CELL ADHESION / 5-Helix bundle / cytoskelatal protein / lipids / structural protein | ||||||
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 / terminal web / cell-substrate junction / 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 / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding / fascia adherens / cell-cell contact zone / apical junction assembly / adherens junction assembly / costamere / regulation of establishment of endothelial barrier / axon extension / protein localization to cell surface / lamellipodium assembly / regulation of focal adhesion assembly / maintenance of blood-brain barrier / brush border / Smooth Muscle Contraction / cell-matrix adhesion / negative regulation of cell migration / cell projection / morphogenesis of an epithelium / adherens junction / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / sarcolemma / platelet aggregation / beta-catenin binding / specific granule lumen / 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 / Signaling by BRAF and RAF1 fusions / cell-cell junction / extracellular vesicle / Signaling by ALK fusions and activated point mutants / 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 / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Chinthalapudi, K. / Izard, T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Differential lipid binding of vinculin isoforms promotes quasi-equivalent dimerization. Authors: Chinthalapudi, K. / Rangarajan, E.S. / Brown, D.T. / Izard, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l0d.cif.gz | 145.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l0d.ent.gz | 115.3 KB | Display | PDB format |
PDBx/mmJSON format | 5l0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/5l0d ftp://data.pdbj.org/pub/pdb/validation_reports/l0/5l0d | HTTPS FTP |
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-Related structure data
Related structure data | 5l0cC 5l0fC 5l0gC 5l0hC 5l0iC 5l0jC 3myiS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19045.068 Da / Num. of mol.: 4 / Fragment: UNP Residues 959-1130 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VCL / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18206 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-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: 49.64 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 3.4 Details: 20 mM citric acid, 80-100 mM Bis-Tris propane (pH 3.4), and 12-16% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Oct 11, 2012 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→100 Å / Num. obs: 19048 / % possible obs: 99.8 % / Redundancy: 8.7 % / Biso Wilson estimate: 51.75 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.048 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 8.2 / CC1/2: 0.987 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MYI Resolution: 2.75→50.13 Å / Cor.coef. Fo:Fc: 0.8875 / Cor.coef. Fo:Fc free: 0.8312 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.378
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Displacement parameters | Biso mean: 53.32 Å2
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Refine analyze | Luzzati coordinate error obs: 0.362 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→50.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.9 Å / Total num. of bins used: 10
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