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Open data
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Basic information
Entry | Database: PDB / ID: 8egx | ||||||
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Title | Complex of Fat4(EC1-4) bound to Dchs1(EC1-4) | ||||||
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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 | ![]() | 183.5 KB | Display | ![]() |
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PDB format | ![]() | 140.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 796.2 KB | Display | ![]() |
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Full document | ![]() | 810.2 KB | Display | |
Data in XML | ![]() | 32 KB | Display | |
Data in CIF | ![]() | 42.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8egwSC ![]() 6vftS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 50777.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
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#2: Protein | Mass: 44963.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
#4: Sugar | ChemComp-NAG / #5: Chemical | ChemComp-CA / Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.25 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M MES, pH 6.5; 0.2 M Sodium Chloride; 10% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Dec 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.688→49.35 Å / Num. obs: 12968 / % possible obs: 95.9 % / Redundancy: 2 % / CC1/2: 0.994 / Net I/σ(I): 4.05 |
Reflection shell | Resolution: 3.688→3.82 Å / Num. unique obs: 1214 / CC1/2: 0.998 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8EGW, 6VFT Resolution: 3.688→49.35 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.29 / 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 | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 168.87 Å2 / Biso mean: 72.4536 Å2 / Biso min: 22.23 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.688→49.35 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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