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- PDB-5l0i: Human metavinculin MVt R975W cardiomyopathy-associated mutant (re... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5l0i | ||||||
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Title | Human metavinculin MVt R975W cardiomyopathy-associated mutant (residues 959-1134) | ||||||
![]() | Vinculin | ||||||
![]() | CELL ADHESION / 5-Helix bundle / cytoskeletal protein / cardiomyopathy | ||||||
Function / homology | ![]() 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 / 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 / maintenance of blood-brain barrier / brush border / Smooth Muscle Contraction / negative regulation of cell migration / cell-matrix adhesion / cell projection / morphogenesis of an epithelium / adherens junction / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / sarcolemma / beta-catenin binding / platelet aggregation / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chinthalapudi, K. / Izard, T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.9 KB | Display | ![]() |
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PDB format | ![]() | 33.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.1 KB | Display | ![]() |
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Full document | ![]() | 445.5 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 13.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5l0cC ![]() 5l0dC ![]() 5l0fC ![]() 5l0gC ![]() 5l0hC ![]() 5l0jC ![]() 3myiS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19648.713 Da / Num. of mol.: 1 / Fragment: UNP Residues 959-1134 / Mutation: R975W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.4 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M Na-citrate tribasic dihydrate, 2% Tacsimate (pH 5), and 16% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 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: 2.45→44.78 Å / Num. obs: 5966 / % possible obs: 98 % / Redundancy: 6.6 % / Biso Wilson estimate: 36.66 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.023 / Net I/σ(I): 49.2 |
Reflection shell | Resolution: 2.45→2.55 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 37 / CC1/2: 0.998 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3MYI Resolution: 2.45→44.78 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.8815 / SU R Cruickshank DPI: 1.208 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.924 / SU Rfree Blow DPI: 0.287 / SU Rfree Cruickshank DPI: 0.287
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Displacement parameters | Biso mean: 39.14 Å2
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Refine analyze | Luzzati coordinate error obs: 0.281 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.45→44.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.74 Å / Total num. of bins used: 5
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