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- PDB-5y04: Crystal Structure of the complex between the vinculin D1 domain a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5y04 | ||||||
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Title | Crystal Structure of the complex between the vinculin D1 domain and alphaE-catenin | ||||||
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![]() | CELL ADHESION / ADHERENS JUNCTION / CYTOSKELETON | ||||||
Function / homology | ![]() small GTPase binding => GO:0031267 / negative regulation of integrin-mediated signaling pathway / VEGFR2 mediated vascular permeability / regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / Smooth Muscle Contraction / MAP2K and MAPK activation / terminal web / RHO GTPases activate IQGAPs ...small GTPase binding => GO:0031267 / negative regulation of integrin-mediated signaling pathway / VEGFR2 mediated vascular permeability / regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / Smooth Muscle Contraction / MAP2K and MAPK activation / terminal web / RHO GTPases activate IQGAPs / Adherens junctions interactions / gamma-catenin binding / epithelial cell-cell adhesion / zonula adherens / gap junction assembly / Platelet degranulation / dystroglycan binding / cellular response to indole-3-methanol / alpha-catenin binding / vinculin binding / flotillin complex / fascia adherens / negative regulation of cell motility / cell-cell contact zone / Myogenesis / adherens junction assembly / apical junction assembly / costamere / regulation of establishment of endothelial barrier / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of smoothened signaling pathway / catenin complex / axon extension / protein localization to cell surface / podosome / negative regulation of protein localization to nucleus / axon regeneration / lamellipodium assembly / regulation of focal adhesion assembly / negative regulation of neuroblast proliferation / smoothened signaling pathway / establishment or maintenance of cell polarity / odontogenesis of dentin-containing tooth / brush border / intercalated disc / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / neuroblast proliferation / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / regulation of cell migration / Neutrophil degranulation / acrosomal vesicle / integrin-mediated signaling pathway / morphogenesis of an epithelium / cell motility / adherens junction / protein localization / sarcolemma / beta-catenin binding / Z disc / cell-cell adhesion / response to estrogen / male gonad development / cell-cell junction / actin filament binding / cell migration / actin cytoskeleton / lamellipodium / regulation of cell population proliferation / cell adhesion / cadherin binding / membrane raft / focal adhesion / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / negative regulation of apoptotic process / structural molecule activity / protein-containing complex / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hirano, Y. / Hakoshima, T. | ||||||
![]() | ![]() Title: The force-sensing device region of alpha-catenin is an intrinsically disordered segment in the absence of intramolecular stabilization of the autoinhibitory form Authors: Hirano, Y. / Amano, Y. / Yonemura, S. / Hakoshima, 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 | ![]() | 126.7 KB | Display | ![]() |
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PDB format | ![]() | 98.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436 KB | Display | ![]() |
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Full document | ![]() | 444.6 KB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xflC ![]() 3w3r 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: 28100.598 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 11410.797 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 276-375 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: 100MM IMIDAZOLE, 0.5-0.7M POTASSIUM TARTRATE, 0.35M SODIUM FORMATE PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 19, 2009 / Details: MIRRORS | ||||||||||||
Radiation | Monochromator: ROTATED-INCLINED DOUBLE-CRYSTAL MONOCHROMATOR , SI (111) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.85→50 Å / Num. obs: 10287 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rsym value: 0.052 / Net I/σ(I): 41.4 | ||||||||||||
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.425 / % possible all: 73.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 94 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→50 Å
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