+Open data
-Basic information
Entry | Database: PDB / ID: 6blq | |||||||||
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Title | Crystal Structure of IAg7 in complex with insulin mimotope p8E9E | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / INSULIN / TYPE I DIABETES / T CELL / AUTOIMMUNE DISEASE | |||||||||
Function / homology | Function and homology information 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 | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Wang, Y. / Dai, S. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6blq.cif.gz | 108.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6blq.ent.gz | 79.2 KB | Display | PDB format |
PDBx/mmJSON format | 6blq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/6blq ftp://data.pdbj.org/pub/pdb/validation_reports/bl/6blq | HTTPS FTP |
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-Related structure data
Related structure data | 5ujtC 6blrC 6blxC 5dmkS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Mus musculus (house mouse) / Gene: H2-Aa / Cell (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04228 |
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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.) Mus musculus (house mouse) / Gene: H2-Ab1 / Cell line (production host): HI5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q31135 |
-Sugars , 2 types, 3 molecules
#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
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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