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- PDB-1g6r: A FUNCTIONAL HOT SPOT FOR ANTIGEN RECOGNITION IN A SUPERAGONIST T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1g6r | ||||||
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Title | A FUNCTIONAL HOT SPOT FOR ANTIGEN RECOGNITION IN A SUPERAGONIST TCR/MHC COMPLEX | ||||||
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![]() | IMMUNE SYSTEM / T CELL ANTIGEN RECEPTOR / MAJOR HISTOCOMPATIBILITY COMPLEX / SUPERAGONIST | ||||||
Function / homology | ![]() alpha-beta T cell receptor complex / 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 / T cell receptor complex / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development ...alpha-beta T cell receptor complex / 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 / T cell receptor complex / 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 / immunoglobulin complex, circulating / immunoglobulin receptor binding / Neutrophil degranulation / complement activation, classical pathway / 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 / antigen binding / 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 / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / antibacterial humoral response / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / blood microparticle / defense response to bacterium / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Degano, M. / Garcia, K.C. / Apostolopoulos, V. / Rudolph, M.G. / Teyton, L. / Wilson, I.A. | ||||||
![]() | ![]() Title: A functional hot spot for antigen recognition in a superagonist TCR/MHC complex. Authors: Degano, M. / Garcia, K.C. / Apostolopoulos, V. / Rudolph, M.G. / Teyton, L. / Wilson, I.A. #1: ![]() Title: Structural basis of plasticity in T cell receptor recognition of a self peptide-MHC antigen Authors: Garcia, K.C. / Degano, M. / Pease, L.R. / Huang, M. / Peterson, P.A. / Teyton, L. / Wilson, I.A. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 320.4 KB | Display | ![]() |
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PDB format | ![]() | 269 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.4 KB | Display | ![]() |
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Full document | ![]() | 573.4 KB | Display | |
Data in XML | ![]() | 51.2 KB | Display | |
Data in CIF | ![]() | 74.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22298.889 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 26284.180 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein | Mass: 31648.322 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Protein | Mass: 11704.359 Da / Num. of mol.: 2 / Fragment: NON-COVALENTLY ASSOCIATED WITH ENTITY 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #5: Protein/peptide | Mass: 1035.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.7 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 7.2 Details: 0.2 M Tris/acetate, 10% PEG 6000, pH 7.2, VAPOR DIFFUSION, temperature 22K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknownDetails: used macroseeding, Garcia, K.C., (1997) Proc.Natl.Acad.Sci.USA., 94, 13838. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 52209 / % possible obs: 83.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 62.4 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.9 / % possible all: 93 |
Reflection | *PLUS Lowest resolution: 50 Å |
Reflection shell | *PLUS % possible obs: 93 % |
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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→50 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 2 % / Rfactor obs: 0.29 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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