+Open data
-Basic information
Entry | Database: PDB / ID: 5l0j | ||||||
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Title | Human vinculin R903Q, D907R, R910T mutant(residues 891-1066) | ||||||
Components | Vinculin | ||||||
Keywords | CELL ADHESION / 5-Helix bundle / cytoskelatal protein / phospholipids / 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 / 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 / regulation of focal adhesion assembly / maintenance of blood-brain barrier / 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 / Signaling by RAF1 mutants / extracellular vesicle / 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 / MOLECULAR REPLACEMENT / Resolution: 4 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 | 5l0j.cif.gz | 76.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l0j.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 5l0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/5l0j ftp://data.pdbj.org/pub/pdb/validation_reports/l0/5l0j | HTTPS FTP |
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-Related structure data
Related structure data | 5l0cC 5l0dC 5l0fC 5l0gC 5l0hC 5l0iC 1rkeS 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: 19716.922 Da / Num. of mol.: 2 / Mutation: R903Q, D907R, R910T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VCL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18206 #2: 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: 4.79 Å3/Da / Density % sol: 74.33 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES sodium (pH 7.5), and 1.5 M Lithium sulfate monohydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2015 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 4→175.2 Å / Num. obs: 6727 / % possible obs: 98.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 105.45 Å2 / Rpim(I) all: 0.043 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 4→4.22 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.9 / CC1/2: 0.896 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RKE Resolution: 4→23.79 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc free: 0.853 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.747
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Displacement parameters | Biso mean: 158.99 Å2
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Refine analyze | Luzzati coordinate error obs: 0 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4→23.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4→4.47 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
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