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Open data
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Basic information
Entry | Database: PDB / ID: 6blq | |||||||||
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Title | Crystal Structure of IAg7 in complex with insulin mimotope p8E9E | |||||||||
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![]() | IMMUNE SYSTEM / INSULIN / TYPE I DIABETES / T CELL / AUTOIMMUNE DISEASE | |||||||||
Function / homology | ![]() antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / antigen processing and presentation / negative regulation of T cell proliferation / multivesicular body / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response ...antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / antigen processing and presentation / negative regulation of T cell proliferation / multivesicular body / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / lysosome / early endosome / lysosomal membrane / external side of plasma membrane / protein-containing complex binding / Golgi apparatus / cell surface / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wang, Y. / Dai, S. | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 108.9 KB | Display | ![]() |
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PDB format | ![]() | 79.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 785.2 KB | Display | ![]() |
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Full document | ![]() | 788.8 KB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 31.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ujtC ![]() 6blrC ![]() 6blxC ![]() 5dmkS 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 , 2 types, 2 molecules AB
#1: Protein | Mass: 21151.549 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 25362.342 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Sugars , 2 types, 3 molecules ![](data/chem/img/NAG.gif)
#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 |
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#4: Sugar |
-Non-polymers , 3 types, 405 molecules ![](data/chem/img/IPA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-IPA / #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | insulin mimotope |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 20% PEG3350, 100mM sodium citrate at pH5.0, 5% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 44763 / % possible obs: 99.8 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 0.48 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5DMK Resolution: 1.8→40.872 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.21
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→40.872 Å
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Refine LS restraints |
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LS refinement shell |
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