[English] 日本語
Yorodumi- PDB-1g6r: A FUNCTIONAL HOT SPOT FOR ANTIGEN RECOGNITION IN A SUPERAGONIST T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g6r | ||||||
---|---|---|---|---|---|---|---|
Title | A FUNCTIONAL HOT SPOT FOR ANTIGEN RECOGNITION IN A SUPERAGONIST TCR/MHC COMPLEX | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / T CELL ANTIGEN RECEPTOR / MAJOR HISTOCOMPATIBILITY COMPLEX / SUPERAGONIST | ||||||
Function / homology | Function and homology information 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 / regulation of membrane depolarization / antigen processing and presentation of exogenous peptide antigen via MHC class I ...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 / regulation of membrane depolarization / 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 / cellular defense response / beta-2-microglobulin binding / 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 / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / T cell differentiation in thymus / iron ion transport / protein refolding / antibacterial humoral response / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / defense response to bacterium / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / innate immune response / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Degano, M. / Garcia, K.C. / Apostolopoulos, V. / Rudolph, M.G. / Teyton, L. / Wilson, I.A. | ||||||
Citation | Journal: Immunity / Year: 2000 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: Journal: Science / Year: 1998 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1g6r.cif.gz | 320.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1g6r.ent.gz | 269 KB | Display | PDB format |
PDBx/mmJSON format | 1g6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/1g6r ftp://data.pdbj.org/pub/pdb/validation_reports/g6/1g6r | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01738 #2: Protein | Mass: 26284.180 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01852 #3: Protein | Mass: 31648.322 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01901 #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.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01887 #5: Protein/peptide | Mass: 1035.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.7 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å |
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 % |
-Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
| ||||||||||||||||
Refine LS restraints |
| ||||||||||||||||
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
|