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Open data
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Basic information
Entry | Database: PDB / ID: 8egw | ||||||
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Title | Complex of Fat4(EC1-4) bound to Dchs1(EC1-3) | ||||||
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![]() | CELL ADHESION / Fat4 / Dachsous1 / Cadherin / Protocadherin / Adhesion / Fat / Dachsous | ||||||
Function / homology | ![]() condensed mesenchymal cell proliferation / mitral valve formation / cell migration involved in endocardial cushion formation / cell-cell adhesion via plasma-membrane adhesion molecules / hippo signaling / pattern specification process / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / post-anal tail morphogenesis / digestive tract development / catenin complex ...condensed mesenchymal cell proliferation / mitral valve formation / cell migration involved in endocardial cushion formation / cell-cell adhesion via plasma-membrane adhesion molecules / hippo signaling / pattern specification process / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / post-anal tail morphogenesis / digestive tract development / catenin complex / cell-cell junction assembly / adherens junction organization / neural tube development / ossification involved in bone maturation / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / branching involved in ureteric bud morphogenesis / cochlea development / homophilic cell adhesion via plasma membrane adhesion molecules / neurogenesis / protein localization to plasma membrane / adherens junction / cell morphogenesis / cerebral cortex development / cell-cell adhesion / apical part of cell / cadherin binding / calcium ion binding / extracellular exosome / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Medina, E. / Luca, V.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the planar cell polarity cadherins Fat4 and Dachsous1. Authors: Medina, E. / Easa, Y. / Lester, D.K. / Lau, E.K. / Sprinzak, D. / Luca, V.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 317.5 KB | Display | ![]() |
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PDB format | ![]() | 252.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 32.2 KB | Display | |
Data in CIF | ![]() | 46.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8egxC ![]() 2a4cS ![]() 3q2wS ![]() 4zi8S ![]() 4zplS ![]() 4zpoS ![]() 5iu9S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 33863.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 50777.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Sugars , 4 types, 5 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / | |
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-Non-polymers , 4 types, 314 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-CA / #8: Chemical | #9: Chemical | ChemComp-EDO / #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.91 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.08 M Magnesium Chloride; 0.1 M Sodium Cacodylate, pH 6.1; 20% Polyethylene Glycol 1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.204→49.085 Å / Num. obs: 50558 / % possible obs: 99.27 % / Redundancy: 3.4 % / CC1/2: 0.995 / Net I/σ(I): 8.87 |
Reflection shell | Resolution: 2.204→2.283 Å / Num. unique obs: 5002 / CC1/2: 0.8 / % possible all: 98.24 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2A4C, 4ZPL, 4ZI8, 4ZPO, 5IU9, 3Q2W Resolution: 2.3→49.083 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→49.083 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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