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Yorodumi- PDB-6duw: Crystal structure of the alpha-N-catenin actin-binding domain H1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6duw | ||||||
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Title | Crystal structure of the alpha-N-catenin actin-binding domain H1 mutant | ||||||
Components | Catenin alpha-2 | ||||||
Keywords | CELL ADHESION / five-helix bundle / F-actin-binding / mechanosensor | ||||||
Function / homology | Function and homology information radial glia guided migration of Purkinje cell / regulation of synapse structural plasticity / negative regulation of Arp2/3 complex-mediated actin nucleation / regulation of neuron migration / catenin complex / brain morphogenesis / dendrite morphogenesis / regulation of neuron projection development / positive regulation of muscle cell differentiation / Myogenesis ...radial glia guided migration of Purkinje cell / regulation of synapse structural plasticity / negative regulation of Arp2/3 complex-mediated actin nucleation / regulation of neuron migration / catenin complex / brain morphogenesis / dendrite morphogenesis / regulation of neuron projection development / positive regulation of muscle cell differentiation / Myogenesis / prepulse inhibition / axonogenesis / adherens junction / structural constituent of cytoskeleton / beta-catenin binding / cell-cell adhesion / actin filament binding / actin cytoskeleton / cell migration / cadherin binding / axon / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Ishiyama, N. / Ikura, M. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Force-dependent allostery of the alpha-catenin actin-binding domain controls adherens junction dynamics and functions. Authors: Ishiyama, N. / Sarpal, R. / Wood, M.N. / Barrick, S.K. / Nishikawa, T. / Hayashi, H. / Kobb, A.B. / Flozak, A.S. / Yemelyanov, A. / Fernandez-Gonzalez, R. / Yonemura, S. / Leckband, D.E. / ...Authors: Ishiyama, N. / Sarpal, R. / Wood, M.N. / Barrick, S.K. / Nishikawa, T. / Hayashi, H. / Kobb, A.B. / Flozak, A.S. / Yemelyanov, A. / Fernandez-Gonzalez, R. / Yonemura, S. / Leckband, D.E. / Gottardi, C.J. / Tepass, U. / Ikura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6duw.cif.gz | 64.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6duw.ent.gz | 37.5 KB | Display | PDB format |
PDBx/mmJSON format | 6duw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6duw_validation.pdf.gz | 423.9 KB | Display | wwPDB validaton report |
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Full document | 6duw_full_validation.pdf.gz | 426.2 KB | Display | |
Data in XML | 6duw_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 6duw_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/6duw ftp://data.pdbj.org/pub/pdb/validation_reports/du/6duw | HTTPS FTP |
-Related structure data
Related structure data | 6duyC 6dv1C 4k1oS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28120.342 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNA2, CAPR / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P26232 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.03 Å3/Da / Density % sol: 69.49 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 2.0 M ammonium sulfate, 10 mM cobalt chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→42.08 Å / Num. obs: 24191 / % possible obs: 99.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 47.58 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.076 / Net I/σ(I): 31.7 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.6 / CC1/2: 0.89 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4K1O Resolution: 2.2→42.08 Å / SU ML: 0.2047 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.4348
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→42.08 Å
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Refine LS restraints |
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LS refinement shell |
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