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- PDB-1oga: A structural basis for immunodominant human T-cell receptor recog... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1oga | ||||||
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Title | A structural basis for immunodominant human T-cell receptor recognition. | ||||||
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![]() | IMMUNE SYSTEM/RECEPTOR / IMMUNE SYSTEM-RECEPTOR-COMPLEX / TCR / MHC / IMMUNODOMINANCE / FLU / COMPLEX / TRANSMEMBRANE / GLYCOPROTEIN / POLYMORPHISM / T-CELL / RECEPTOR / IMMUNE SYSTEM-RECEPTOR complex | ||||||
Function / homology | ![]() : / : / regulation of membrane depolarization / alpha-beta T cell receptor complex / retina homeostasis / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation ...: / : / regulation of membrane depolarization / alpha-beta T cell receptor complex / retina homeostasis / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / alpha-beta T cell activation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / Generation of second messenger molecules / TAP binding / protection from natural killer cell mediated cytotoxicity / PD-1 signaling / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen binding / response to bacterium / 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 / ER to Golgi transport vesicle membrane / 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 / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / Downstream TCR signaling / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / cellular response to lipopolysaccharide / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stewart-Jones, G.B.E. / McMichael, A.J. / Bell, J.I. / Stuart, D.I. / Jones, E.Y. | ||||||
![]() | ![]() Title: A Structural Basis for Immunodominant Human T Cell Receptor Recognition Authors: Stewart-Jones, G.B.E. / Mcmichael, A.J. / Bell, J.I. / Stuart, D.I. / Jones, E.Y. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 191.7 KB | Display | ![]() |
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PDB format | ![]() | 150.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.7 KB | Display | ![]() |
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Full document | ![]() | 487.7 KB | Display | |
Data in XML | ![]() | 38.2 KB | Display | |
Data in CIF | ![]() | 55.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qsfS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31951.316 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR ALPHA-1, -2, -3, RESIDUES 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: REFOLDED FROM INCLUSION BODIES. REFOLDED FROM INCLUSION BODIES Production host: ![]() ![]() |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: BETA-2-MICROGLOBULIN, RESIDUES 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: REFOLDED FROM INCLUSION BODIES. REFOLDED FROM INCLUSION BODIES Production host: ![]() ![]() |
-T-CELL RECEPTOR ... , 2 types, 2 molecules DE
#4: Protein | Mass: 23599.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: CONTAINS ALSO C (CONSTANT) REGION / Source: (gene. exp.) ![]() Description: REFOLDED FROM INCLUSION BODIES. REFOLDED FROM INCLUSION BODIES Production host: ![]() ![]() |
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#5: Protein | Mass: 28559.518 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR, RESIDUES 1-130 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: REFOLDED FROM INCLUSION BODIES. REFOLDED FROM INCLUSION BODIES Production host: ![]() ![]() |
-Protein/peptide / Non-polymers , 2 types, 569 molecules C![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#3: Protein/peptide | Mass: 966.174 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: REFOLDED FROM INCLUSION BODIES. PEPTIDE CHAIN C.REFOLDED FROM INCLUSION BODIES Source: (synth.) ![]() |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 41.5 % | ||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: 14% PEG8000, 50MM MES PH 6.5 | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||
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: ADSC CCD / Detector: CCD / Date: Aug 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. obs: 200813 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 17.4 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 38.5 |
Reflection shell | Resolution: 1.4→1.45 Å / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.9 / % possible all: 98.3 |
Reflection | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 30 Å / Num. measured all: 3465000 / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS % possible obs: 98.3 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QSF Resolution: 1.4→29.98 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 199296.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: RESOLUTION-DEPENDENT WEIGHTING, BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.2662 Å2 / ksol: 0.371397 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→29.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.45 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 30 Å / Num. reflection obs: 178426 / Rfactor Rfree: 0.232 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.369 / Rfactor Rwork: 0.364 / Num. reflection Rwork: 9329 |