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Open data
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Basic information
Entry | Database: PDB / ID: 4irj | |||||||||
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Title | Structure of the mouse CD1d-4ClPhC-alpha-GalCer-iNKT TCR complex | |||||||||
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![]() | IMMUNE SYSTEM / antigen presentation / glycolipid / NKT cells | |||||||||
Function / homology | ![]() regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive thymic T cell selection ...regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive thymic T cell selection / positive regulation of macrophage activation / 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 / positive regulation of interleukin-4 production / antigen processing and presentation / regulation of immune response / cellular defense response / T cell receptor binding / positive regulation of interleukin-2 production / Neutrophil degranulation / 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 / positive regulation of type II interferon production / 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 / late endosome / 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 / early endosome / lysosome / endosome membrane / immune response / external side of plasma membrane / lysosomal membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Nemcovic, M. / Zajonc, D.M. | |||||||||
![]() | ![]() Title: Enhanced TCR footprint by a novel glycolipid increases NKT-dependent tumor protection. Authors: Aspeslagh, S. / Nemcovic, M. / Pauwels, N. / Venken, K. / Wang, J. / Van Calenbergh, S. / Zajonc, D.M. / Elewaut, D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 168.2 KB | Display | ![]() |
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PDB format | ![]() | 134 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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1 |
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Unit cell |
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Components
-Protein , 3 types, 3 molecules ABD
#1: Protein | Mass: 32632.668 Da / Num. of mol.: 1 / Fragment: UNP residues 19-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 11660.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Protein | Mass: 27026.998 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens Gene: Vbeta8.2 (mouse variable domain, human constant domain) Plasmid: pET22b / Production host: ![]() ![]() |
-Antibody , 1 types, 1 molecules C
#3: Antibody | Mass: 23055.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens Gene: Valpha14 (mouse variable domain, human constant domain) Plasmid: pET22b / Production host: ![]() ![]() |
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-Sugars , 2 types, 3 molecules ![](data/chem/img/NAG.gif)
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose |
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#6: Sugar |
-Non-polymers , 2 types, 14 molecules ![](data/chem/img/1L9.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-1L9 / |
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#8: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.73 % |
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Crystal grow | Temperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% polyethylene glycol 4000, 0.2M sodium thiocyanate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 1, 2012 |
Radiation | Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795706 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 22997 / Num. obs: 21794 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3→3.11 Å / % possible all: 100 |
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Processing
Software | Name: REFMAC / Version: 5.6.0104 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]()
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.883 Å2
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Refinement step | Cycle: LAST / Resolution: 3→38.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.001→3.078 Å / Total num. of bins used: 20
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