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- PDB-6r0e: Structure of F11TCR in complex with DR1 MHC Class II presenting P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6r0e | ||||||
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Title | Structure of F11TCR in complex with DR1 MHC Class II presenting PKYVKQNTLKLAT | ||||||
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![]() | IMMUNE SYSTEM / FLU / MHC Class II / Human / DR1 / HLA-DR1 / 3D | ||||||
Function / homology | ![]() regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation ...regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / inflammatory response to antigenic stimulus / positive regulation of kinase activity / intermediate filament / transport vesicle membrane / polysaccharide binding / T-helper 1 type immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / T cell receptor binding / negative regulation of T cell proliferation / detection of bacterium / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / viral budding from plasma membrane / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / 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 / T cell receptor signaling pathway / early endosome membrane / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of viral entry into host cell / lysosome / host cell surface receptor binding / immune response / positive regulation of protein phosphorylation / external side of plasma membrane / Golgi membrane / fusion of virus membrane with host plasma membrane / lysosomal membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / positive regulation of DNA-templated transcription / virion membrane / cell surface / signal transduction / extracellular space / extracellular exosome / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rizkallah, P.J. / Greenshields-Watson, A.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: CD4+T Cells Recognize Conserved Influenza A Epitopes through Shared Patterns of V-Gene Usage and Complementary Biochemical Features. Authors: Greenshields-Watson, A. / Attaf, M. / MacLachlan, B.J. / Whalley, T. / Rius, C. / Wall, A. / Lloyd, A. / Hughes, H. / Strange, K.E. / Mason, G.H. / Schauenburg, A.J. / Hulin-Curtis, S.L. / ...Authors: Greenshields-Watson, A. / Attaf, M. / MacLachlan, B.J. / Whalley, T. / Rius, C. / Wall, A. / Lloyd, A. / Hughes, H. / Strange, K.E. / Mason, G.H. / Schauenburg, A.J. / Hulin-Curtis, S.L. / Geary, J. / Chen, Y. / Lauder, S.N. / Smart, K. / Vijaykrishna, D. / Grau, M.L. / Shugay, M. / Andrews, R. / Dolton, G. / Rizkallah, P.J. / Gallimore, A.M. / Sewell, A.K. / Godkin, A.J. / Cole, D.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 333.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6qzaC ![]() 6qzcC ![]() 6qzdC ![]() 1fytS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-HLA class II histocompatibility antigen, ... , 2 types, 2 molecules AAABBB
#1: Protein | Mass: 21287.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 22211.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules CCC
#3: Protein/peptide | Mass: 1506.807 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Protein , 2 types, 2 molecules DDDEEE
#4: Protein | Mass: 22438.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#5: Protein | Mass: 27208.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 317 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-SO4 / | #8: Chemical | #9: 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: 3.24 Å3/Da / Density % sol: 62.07 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6 / Details: 0.1 M Na Cacodylate, 0.2 M NH4 SO4, 15 % PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97623 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→92.46 Å / Num. obs: 96543 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 39.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.031 / Rrim(I) all: 0.084 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.91→1.96 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.26 / Num. unique obs: 7001 / Rpim(I) all: 0.491 / Rrim(I) all: 1.354 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1FYT Resolution: 1.91→92.45 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.21 / SU B: 7.516 / SU ML: 0.105 / Average fsc free: 0.903 / Average fsc work: 0.9121 / Cross valid method: FREE R-VALUE / ESU R: 0.132 / ESU R Free: 0.125 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.547 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→92.45 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / 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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