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- PDB-5ujt: Crystal structure of human HLA-DQ8 in complex with insulin mimoto... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ujt | |||||||||
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Title | Crystal structure of human HLA-DQ8 in complex with insulin mimotope binding in register 3 | |||||||||
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![]() | IMMUNE SYSTEM / INSULIN / TYPE I DIABETES / T CELL / AUTOIMMUNE DISEASE | |||||||||
Function / homology | ![]() antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II protein complex / adaptive immune response / membrane => GO:0016020 / endosome membrane / lysosomal membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wang, Y. / Dai, S. | |||||||||
![]() | ![]() Title: C-terminal modification of the insulin B:11-23 peptide creates superagonists in mouse and human type 1 diabetes. Authors: Wang, Y. / Sosinowski, T. / Novikov, A. / Crawford, F. / Neau, D.B. / Yang, J. / Kwok, W.W. / Marrack, P. / Kappler, J.W. / Dai, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 255.7 KB | Display | ![]() |
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PDB format | ![]() | 204.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1003.4 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 50.4 KB | Display | |
Data in CIF | ![]() | 71.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6blqC ![]() 6blrC ![]() 6blxC ![]() 1jk8S 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-MHC class II ... , 2 types, 6 molecules ADGBEH
#1: Protein | Mass: 21138.500 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 22246.021 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Protein/peptide / Non-polymers , 2 types, 648 molecules CFI![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#3: Protein/peptide | Mass: 1581.701 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #6: Water | ChemComp-HOH / | |
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-Sugars , 2 types, 4 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[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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#5: Sugar |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.59 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 15% PEG3350, 100mM Tacsimate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→79.868 Å / Num. obs: 118542 / % possible obs: 99.6 % / Redundancy: 2 % / Net I/σ(I): 50 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JK8 Resolution: 1.94→79.87 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→79.87 Å
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Refine LS restraints |
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LS refinement shell |
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