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Open data
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Basic information
Entry | Database: PDB / ID: 4k1o | ||||||
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Title | Crystal structure of the alphaN-catenin actin-binding domain | ||||||
![]() | Catenin alpha-2 | ||||||
![]() | CELL ADHESION / five-helix bundle / F-actin / alpha-catenin | ||||||
Function / homology | ![]() radial glia guided migration of Purkinje cell / extrinsic component of postsynaptic membrane / regulation of synapse structural plasticity / extrinsic component of presynaptic membrane / modification of postsynaptic actin cytoskeleton / negative regulation of Arp2/3 complex-mediated actin nucleation / regulation of neuron migration / presynaptic active zone cytoplasmic component / Myogenesis / catenin complex ...radial glia guided migration of Purkinje cell / extrinsic component of postsynaptic membrane / regulation of synapse structural plasticity / extrinsic component of presynaptic membrane / modification of postsynaptic actin cytoskeleton / negative regulation of Arp2/3 complex-mediated actin nucleation / regulation of neuron migration / presynaptic active zone cytoplasmic component / Myogenesis / catenin complex / brain morphogenesis / parallel fiber to Purkinje cell synapse / dendrite morphogenesis / regulation of neuron projection development / postsynaptic density, intracellular component / prepulse inhibition / hippocampal mossy fiber to CA3 synapse / axonogenesis / adherens junction / beta-catenin binding / cell-cell adhesion / actin filament binding / cell migration / actin cytoskeleton / lamellipodium / basolateral plasma membrane / postsynaptic density / cadherin binding / axon / structural molecule activity / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ishiyama, N. / Ikura, M. | ||||||
![]() | ![]() Title: An autoinhibited structure of alpha-catenin and its implications for vinculin recruitment to adherens junctions. Authors: Ishiyama, N. / Tanaka, N. / Abe, K. / Yang, Y.J. / Abbas, Y.M. / Umitsu, M. / Nagar, B. / Bueler, S.A. / Rubinstein, J.L. / Takeichi, M. / Ikura, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 53.1 KB | Display | ![]() |
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PDB format | ![]() | 36.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.1 KB | Display | ![]() |
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Full document | ![]() | 433.5 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 11.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29102.627 Da / Num. of mol.: 1 / Fragment: C-terminal actin-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE CRYSTALLIZ | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.99 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7 Details: 0.1M HEPES, pH 7.0, 1.6 M (NH4)2SO4, 0.2 M NaCl,and 0.1M K/Na tartate, vapor diffusion, temperature 277K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.6→50 Å / Num. all: 12400 / Num. obs: 12361 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 70.6 Å2 / Rsym value: 0.049 / Χ2: 1.08 / Net I/σ(I): 16.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.03 Å2 / Biso mean: 70.8448 Å2 / Biso min: 47.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.603→39.736 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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