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Open data
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Basic information
Entry | Database: PDB / ID: 7qhp | ||||||||||||
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Title | Structure of I-Ag7 with a bound hybrid insulin peptide | ||||||||||||
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![]() | IMMUNE SYSTEM / Diabetes / MHC class II / hybrid insulin peptide / autoimmune disease | ||||||||||||
Function / homology | ![]() glucose transmembrane transport / antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / transmembrane receptor protein tyrosine kinase activator activity / regulation of protein secretion ...glucose transmembrane transport / antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / transmembrane receptor protein tyrosine kinase activator activity / regulation of protein secretion / positive regulation of respiratory burst / antigen processing and presentation / negative regulation of acute inflammatory response / alpha-beta T cell activation / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / negative regulation of lipid catabolic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of T cell proliferation / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / response to cAMP / neuron projection maintenance / positive regulation of protein metabolic process / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / response to cytokine / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of proteolysis / cellular response to glucose stimulus / insulin-like growth factor receptor binding / wound healing / insulin receptor binding / negative regulation of protein catabolic process / hormone activity / receptor internalization / peptide antigen assembly with MHC class II protein complex / positive regulation of protein localization to nucleus / MHC class II protein complex / vasodilation / glucose metabolic process / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / regulation of protein localization / positive regulation of immune response / positive regulation of T cell activation / insulin receptor signaling pathway / MHC class II protein complex binding / glucose homeostasis / late endosome membrane / secretory granule lumen / collagen-containing extracellular matrix / adaptive immune response / protease binding / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / lysosome / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / negative regulation of gene expression / positive regulation of cell population proliferation / protein-containing complex binding / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Lopez-Sagaseta, J. / Erausquin, E. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural plasticity in I-A g7 links autoreactivity to hybrid insulin peptides in type I diabetes. Authors: Erausquin, E. / Serra, P. / Parras, D. / Santamaria, P. / Lopez-Sagaseta, J. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.3 KB | Display | ![]() |
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PDB format | ![]() | 71.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.3 KB | Display | ![]() |
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Full document | ![]() | 455.6 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7z50C ![]() 1mujS 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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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 23027.711 Da / Num. of mol.: 1 / Mutation: I91C Source method: isolated from a genetically manipulated source Details: This polypeptide corresponds to the alpha chain of a murine major histocompatibility complex (MHC) class II molecule. Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 26263.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Hybrid insulin peptide covalently bound through glycine-serine linker to N-terminal of polypeptide Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules T
#3: Protein/peptide | Mass: 1445.591 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: This peptide represents the result of a fusion of fragments derived from chromogranin A and insulin C. Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 300 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.17 M ammonium sulfate, 25% w/v PEG 4000, 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2021 |
Radiation | Monochromator: Si(111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979185 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→70.254 Å / Num. obs: 44356 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 29.68 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.036 / Rrim(I) all: 0.084 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 4.939→70.254 Å / Rmerge(I) obs: 0.037 / Mean I/σ(I) obs: 30.4 / Num. unique obs: 2365 / CC1/2: 0.998 / Rpim(I) all: 0.018 / Rrim(I) all: 0.042 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1MUJ Resolution: 1.82→54.41 Å / SU ML: 0.207 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.1636 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→54.41 Å
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Refine LS restraints |
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LS refinement shell |
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