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Open data
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Basic information
Entry | Database: PDB / ID: 6u3n | ||||||
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Title | LS2.8/3.15 - DQ2-P.fluor-alpha1a complex | ||||||
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![]() | IMMUNE SYSTEM / Immune Complex / Celiac disease / Gliadin epitope / TCR cross-reactivity | ||||||
Function / homology | ![]() MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / PD-1 signaling / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane ...MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / PD-1 signaling / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / 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 / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / endosome membrane / immune response / lysosomal membrane / Golgi membrane / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Petersen, J. / Rossjohn, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: T cell receptor cross-reactivity between gliadin and bacterial peptides in celiac disease. Authors: Petersen, J. / Ciacchi, L. / Tran, M.T. / Loh, K.L. / Kooy-Winkelaar, Y. / Croft, N.P. / Hardy, M.Y. / Chen, Z. / McCluskey, J. / Anderson, R.P. / Purcell, A.W. / Tye-Din, J.A. / Koning, F. ...Authors: Petersen, J. / Ciacchi, L. / Tran, M.T. / Loh, K.L. / Kooy-Winkelaar, Y. / Croft, N.P. / Hardy, M.Y. / Chen, Z. / McCluskey, J. / Anderson, R.P. / Purcell, A.W. / Tye-Din, J.A. / Koning, F. / Reid, H.H. / Rossjohn, 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 | ![]() | 358.4 KB | Display | ![]() |
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PDB format | ![]() | 281.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.3 KB | Display | ![]() |
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Full document | ![]() | 457.3 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 26 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
-T-CELL RECEPTOR, LS2.8/3.15 ... , 2 types, 2 molecules DE
#1: Protein | Mass: 22893.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 27528.615 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-MHC class II HLA-DQ- ... , 2 types, 2 molecules AB
#3: Protein | Mass: 21501.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#4: Protein | Mass: 23703.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein/peptide / Sugars / Non-polymers , 3 types, 3 molecules C![](data/chem/img/NAG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/HOH.gif)
#5: Protein/peptide | Mass: 2044.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#6: Sugar | ChemComp-NAG / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 22% PEG3350, 0.2M Na-K Tartrate, 0.1M MES pH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9464 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→46.48 Å / Num. obs: 53350 / % possible obs: 99.91 % / Redundancy: 2 % / Rpim(I) all: 0.02771 / Net I/σ(I): 17.05 |
Reflection shell | Resolution: 2.8→2.9 Å / Mean I/σ(I) obs: 1.85 / Num. unique obs: 5211 / Rpim(I) all: 0.4184 / % possible all: 99.92 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.8→46.48 Å
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