+Open data
-Basic information
Entry | Database: PDB / ID: 4k1o | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the alphaN-catenin actin-binding domain | ||||||
Components | Catenin alpha-2CTNNA2 | ||||||
Keywords | CELL ADHESION / five-helix bundle / F-actin / alpha-catenin | ||||||
Function / homology | Function and homology information 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 / brain morphogenesis ...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 / brain morphogenesis / catenin complex / 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 / cell-cell adhesion / beta-catenin binding / cell migration / actin filament binding / actin cytoskeleton / lamellipodium / basolateral plasma membrane / postsynaptic density / cadherin binding / axon / structural molecule activity / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.603 Å | ||||||
Authors | Ishiyama, N. / Ikura, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4k1o.cif.gz | 53.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4k1o.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 4k1o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/4k1o ftp://data.pdbj.org/pub/pdb/validation_reports/k1/4k1o | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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.) Mus musculus (house mouse) / Gene: Catna2, Ctnna2 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus / References: UniProt: Q61301 | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE CRYSTALLIZ | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.99 % |
---|---|
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 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.603→39.736 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7918 / SU ML: 0.26 / σ(F): 0 / Phase error: 27.25 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
|