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Open data
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Basic information
Entry | Database: PDB / ID: 7sg0 | ||||||
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Title | W316 TCR in complex with HLA-DQ2-omega1 | ||||||
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![]() | IMMUNE SYSTEM / TCR-pHLA complex / Celiac disease | ||||||
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 / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / adaptive immune response / endosome membrane / immune response / Golgi membrane / lysosomal membrane / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ciacchi, L. / Farenc, C. / Petersen, J. / Reid, H.H. / Rossjohn, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of T cell receptor specificity and cross-reactivity of two HLA-DQ2.5-restricted gluten epitopes in celiac disease. Authors: Ciacchi, L. / Farenc, C. / Dahal-Koirala, S. / Petersen, J. / Sollid, L.M. / 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 | ![]() | 335.7 KB | Display | ![]() |
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PDB format | ![]() | 270.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7sg1C ![]() 7sg2C ![]() 4ozhS ![]() 6cugS ![]() 6mffS 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: 20683.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 23700.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-T-cell receptor, w316, ... , 2 types, 2 molecules DE
#4: Protein | Mass: 22880.271 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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#5: Protein | Mass: 26937.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
-Protein/peptide / Sugars / Non-polymers , 3 types, 6 molecules C![](data/chem/img/NAG.gif)
![](data/chem/img/EDO.gif)
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#3: Protein/peptide | Mass: 1311.437 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
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#6: Sugar | #7: Chemical | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.6 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 24% PEG3350, 0.25 M (NH4)2SO4 and 0.1 M Tris/HCl at pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2020 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 3→48.52 Å / Num. obs: 22108 / % possible obs: 99.8 % / Redundancy: 2 % / CC1/2: 0.919 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2177 / CC1/2: 0.384 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6MFF, 6CUG, 4OZH Resolution: 3→48.52 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 154.86 Å2 / Biso mean: 55.2196 Å2 / Biso min: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→48.52 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 63.2724 Å / Origin y: -71.0908 Å / Origin z: 21.0647 Å
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Refinement TLS group |
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