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Open data
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Basic information
Entry | Database: PDB / ID: 4ozh | ||||||
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Title | S16 protein complex | ||||||
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![]() | IMMUNE SYSTEM / IMMUNE RECEPTOR-LIGAND COMPLEX | ||||||
Function / homology | ![]() nutrient reservoir activity / MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / alpha-beta T cell receptor complex / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling ...nutrient reservoir activity / MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / alpha-beta T cell receptor complex / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / immunoglobulin complex, circulating / immunoglobulin receptor binding / MHC class II antigen presentation / trans-Golgi network membrane / complement activation, classical pathway / lumenal side of endoplasmic reticulum membrane / antigen binding / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / T cell receptor signaling pathway / antibacterial humoral response / adaptive immune response / blood microparticle / endosome membrane / immune response / lysosomal membrane / Golgi membrane / extracellular exosome / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Petersen, J. / Reid, H.H. / Rossjohn, J. | ||||||
![]() | ![]() Title: T-cell receptor recognition of HLA-DQ2-gliadin complexes associated with celiac disease. Authors: Petersen, J. / Montserrat, V. / Mujico, J.R. / Loh, K.L. / Beringer, D.X. / van Lummel, M. / Thompson, A. / Mearin, M.L. / Schweizer, J. / Kooy-Winkelaar, Y. / van Bergen, J. / Drijfhout, J. ...Authors: Petersen, J. / Montserrat, V. / Mujico, J.R. / Loh, K.L. / Beringer, D.X. / van Lummel, M. / Thompson, A. / Mearin, M.L. / Schweizer, J. / Kooy-Winkelaar, Y. / van Bergen, J. / Drijfhout, J.W. / Kan, W.T. / La Gruta, N.L. / Anderson, R.P. / Reid, H.H. / Koning, F. / 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 | ![]() | 648.6 KB | Display | ![]() |
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PDB format | ![]() | 537.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 526.3 KB | Display | ![]() |
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Full document | ![]() | 540.5 KB | Display | |
Data in XML | ![]() | 53.8 KB | Display | |
Data in CIF | ![]() | 74.3 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-HLA class II histocompatibility antigen, DQ ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 21517.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 24361.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-T-cell receptor, s16, ... , 2 types, 4 molecules EGFH
#3: Protein | Mass: 22563.098 Da / Num. of mol.: 2 / Mutation: T176C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 26911.725 Da / Num. of mol.: 2 / Mutation: C202A, S184C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Protein/peptide / Sugars , 2 types, 5 molecules IJ![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#5: Protein/peptide | Mass: 1380.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #6: Sugar | |
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-Non-polymers , 2 types, 41 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-CA / |
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#8: Water | ChemComp-HOH / |
-Details
Sequence details | The authors state that there are mutations T176C in T-cell receptor, s16, alpha chain, C202A, S184C ...The authors state that there are mutations T176C in T-cell receptor, s16, alpha chain, C202A, S184C in T-cell receptor, s16, beta chain. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.89 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: Mother liquor: 0.15- 0.25M CaOAc, 0.1 M Tris/HCl, 12-18% PEG3350, Additives: 2-3 mM reduced and oxidised Glutathione PH range: 8.0-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→40.99 Å / Num. obs: 43700 / % possible obs: 93.22 % / Redundancy: 2 % / Biso Wilson estimate: 76.05 Å2 / Rmerge(I) obs: 0.04927 / Net I/σ(I): 2 |
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Processing
Software | Name: BUSTER / Version: 2.10.0 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.8→40.99 Å / Cor.coef. Fo:Fc: 0.8982 / Cor.coef. Fo:Fc free: 0.8859 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.364
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Displacement parameters | Biso mean: 66 Å2
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Refine analyze | Luzzati coordinate error obs: 0.473 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.8→40.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.87 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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