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Open data
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Basic information
Entry | Database: PDB / ID: 1l7c | ||||||
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Title | alpha-catenin fragment, residues 385-651 | ||||||
![]() | Alpha E-catenin | ||||||
![]() | CELL ADHESION / four-helix bundle | ||||||
Function / homology | ![]() negative regulation of integrin-mediated signaling pathway / CDH11 homotypic and heterotypic interactions / VEGFR2 mediated vascular permeability / Regulation of CDH19 Expression and Function / Regulation of CDH11 function / RHO GTPases activate IQGAPs / Adherens junctions interactions / gamma-catenin binding / epithelial cell-cell adhesion / zonula adherens ...negative regulation of integrin-mediated signaling pathway / CDH11 homotypic and heterotypic interactions / VEGFR2 mediated vascular permeability / Regulation of CDH19 Expression and Function / Regulation of CDH11 function / RHO GTPases activate IQGAPs / Adherens junctions interactions / gamma-catenin binding / epithelial cell-cell adhesion / zonula adherens / gap junction assembly / cellular response to indole-3-methanol / vinculin binding / flotillin complex / negative regulation of cell motility / Myogenesis / apical junction assembly / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of smoothened signaling pathway / Adherens junctions interactions / catenin complex / negative regulation of protein localization to nucleus / axon regeneration / negative regulation of neuroblast proliferation / smoothened signaling pathway / establishment or maintenance of cell polarity / Myogenesis / odontogenesis of dentin-containing tooth / intercalated disc / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / neuroblast proliferation / RHO GTPases activate IQGAPs / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / acrosomal vesicle / VEGFR2 mediated vascular permeability / integrin-mediated signaling pathway / cell motility / adherens junction / protein localization / beta-catenin binding / cell-cell adhesion / response to estrogen / male gonad development / cell-cell junction / actin filament binding / cell migration / actin cytoskeleton / lamellipodium / cell junction / regulation of cell population proliferation / cell adhesion / cadherin binding / intracellular membrane-bounded organelle / focal adhesion / apoptotic process / protein-containing complex binding / negative regulation of apoptotic process / structural molecule activity / RNA binding / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pokutta, S. / Drees, F. / Takai, Y. / Nelson, W.J. / Weis, W.I. | ||||||
![]() | ![]() Title: Biochemical and structural definition of the l-afadin- and actin-binding sites of alpha-catenin. Authors: Pokutta, S. / Drees, F. / Takai, Y. / Nelson, W.J. / Weis, W.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141 KB | Display | ![]() |
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PDB format | ![]() | 118.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.7 KB | Display | ![]() |
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Full document | ![]() | 473.1 KB | Display | |
Data in XML | ![]() | 27.9 KB | Display | |
Data in CIF | ![]() | 38.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 30206.965 Da / Num. of mol.: 3 / Fragment: Residues 385-651 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.23 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: sodium acetate, dithiothreitol, urea, sodium/potassium tartrate, isopropanol, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 24, 1999 / Details: double flat monochromator + mirror | |||||||||||||||
Radiation | Monochromator: Null / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→30 Å / Num. all: 56243 / Num. obs: 54918 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 19.3 | |||||||||||||||
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.237 / Num. unique all: 2734 / % possible all: 100 | |||||||||||||||
Reflection | *PLUS Rmerge(I) obs: 0.037 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.248 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.5627 Å2 / ksol: 0.339732 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor obs: 0.238 / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.238 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.342 / Rfactor Rwork: 0.286 / Rfactor obs: 0.286 |