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Open data
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Basic information
Entry | Database: PDB / ID: 5iry | |||||||||
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Title | Crystal structure of human Desmocollin-1 ectodomain | |||||||||
![]() | Desmocollin-1 | |||||||||
![]() | CELL ADHESION / extracellular cadherin domain / desmosome / cell surface | |||||||||
Function / homology | ![]() Keratinization / desmosome / Formation of the cornified envelope / cornified envelope / gap junction / homophilic cell adhesion via plasma membrane adhesion molecules / ficolin-1-rich granule membrane / cell-cell adhesion / cell-cell junction / membrane => GO:0016020 ...Keratinization / desmosome / Formation of the cornified envelope / cornified envelope / gap junction / homophilic cell adhesion via plasma membrane adhesion molecules / ficolin-1-rich granule membrane / cell-cell adhesion / cell-cell junction / membrane => GO:0016020 / calcium ion binding / Neutrophil degranulation / extracellular exosome / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Brasch, J. / Harrison, O.J. / Shapiro, L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of adhesive binding by desmocollins and desmogleins. Authors: Harrison, O.J. / Brasch, J. / Lasso, G. / Katsamba, P.S. / Ahlsen, G. / Honig, B. / Shapiro, L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 416.9 KB | Display | ![]() |
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PDB format | ![]() | 345.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5eqxC ![]() 5erdC ![]() 5erpC ![]() 5j5jC ![]() 3q2vS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 61896.742 Da / Num. of mol.: 2 / Fragment: unp residues 135-676 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 3 types, 11 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/MAN.gif)
![](data/chem/img/MAN.gif)
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Sugar | ChemComp-NAG / |
#5: Sugar | ChemComp-MAN / |
-Non-polymers , 3 types, 37 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CA / #6: Chemical | ChemComp-EDO / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% (w/v) PEG20000, 0.1M Tris-Bicine pH8.5, 5% (v/v) ethyleneglycol, 0.06M Calcium chloride, 20% (w/v) glycerol (cryoprotectant, added before freezing) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 11, 2015 |
Radiation | Monochromator: Cryo-Cooled double Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.095→19.994 Å / Num. obs: 28445 / % possible obs: 99.1 % / Redundancy: 4.2 % / Net I/σ(I): 9.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3q2v Resolution: 3.095→19.994 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.095→19.994 Å
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Refine LS restraints |
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LS refinement shell |
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