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- PDB-3rgv: A single TCR bound to MHCI and MHC II reveals switchable TCR conf... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3rgv | ||||||
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Title | A single TCR bound to MHCI and MHC II reveals switchable TCR conformers | ||||||
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![]() | IMMUNE SYSTEM / TCR / MHC / MHC class I | ||||||
Function / homology | ![]() Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / peptide binding / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to bacterium / immune response / external side of plasma membrane / lysosomal membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dai, S. / Huseby, E. / Scott-Browne, J. / Rubtsova, K. / Pinilla, C. / Crawford, F. / Marrack, P. / Yin, L. / Kappler, J.W. | ||||||
![]() | ![]() Title: A Single T Cell Receptor Bound to Major Histocompatibility Complex Class I and Class II Glycoproteins Reveals Switchable TCR Conformers. Authors: Yin, L. / Huseby, E. / Scott-Browne, J. / Rubtsova, K. / Pinilla, C. / Crawford, F. / Marrack, P. / Dai, S. / Kappler, J.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175 KB | Display | ![]() |
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PDB format | ![]() | 138.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 22206.318 Da / Num. of mol.: 1 / Mutation: Y84C, C121S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 26471.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 31701.340 Da / Num. of mol.: 1 / Fragment: Residues 22-296 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Protein | Mass: 11761.411 Da / Num. of mol.: 1 / Fragment: Residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#5: Protein/peptide | Mass: 1489.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.83 Å3/Da / Density % sol: 67.95 % |
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Crystal grow | Temperature: 298 K / Method: hanging drop / pH: 7 / Details: PEG 3350, pH 7, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→19.43 Å / Num. all: 34349 / Num. obs: 30372 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3C60 and 2ZSV Resolution: 2.9→19.43 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7944 / SU ML: 2.4 / σ(F): 0.1 / 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 / Bsol: 20.892 Å2 / ksol: 0.285 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 131.24 Å2 / Biso mean: 58.9744 Å2 / Biso min: 24.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→19.43 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: 11
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