+Open data
-Basic information
Entry | Database: PDB / ID: 4irs | |||||||||
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Title | Structure of the mouse CD1d-PyrC-alpha-GalCer-iNKT TCR complex | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / antigen presentation / glycolipid / NKT cells | |||||||||
Function / homology | Function and homology information regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / lipid antigen binding / 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 ...regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / lipid antigen binding / 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 / alpha-beta T cell receptor complex / 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 / regulation of membrane depolarization / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / antigen processing and presentation / PD-1 signaling / positive regulation of interleukin-4 production / regulation of immune response / cellular defense response / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / Neutrophil degranulation / cell adhesion molecule binding / T cell receptor binding / response to bacterium / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / response to molecule of bacterial origin / regulation of erythrocyte differentiation / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / late endosome / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / histone binding / T cell receptor signaling pathway / protein refolding / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / adaptive immune response / lysosome / learning or memory / early endosome / endosome membrane / defense response to Gram-positive bacterium / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Nemcovic, M. / Zajonc, D.M. | |||||||||
Citation | Journal: J.Immunol. / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4irs.cif.gz | 174.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4irs.ent.gz | 139.6 KB | Display | PDB format |
PDBx/mmJSON format | 4irs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/4irs ftp://data.pdbj.org/pub/pdb/validation_reports/ir/4irs | HTTPS FTP |
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-Related structure data
-Links
-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.) Mus musculus (house mouse) / Gene: Cd1.1, CD1d, Cd1d1 / Plasmid: pBACp10pH / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P11609 |
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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.) Mus musculus (house mouse) / Gene: B2m, beta-2-microglobulin / Plasmid: pBACp10pH / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P01887 |
#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: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 |
-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: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P01848*PLUS |
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-Sugars , 3 types, 3 molecules
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#7: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 113 molecules
#8: Chemical | ChemComp-1LA / |
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#9: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.37 % |
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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 di-ammonium hydrogen citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2012 |
Radiation | Monochromator: Curved crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→59.33 Å / Num. all: 28024 / Num. obs: 26546 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.8→2.95 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→59.33 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.89 / SU B: 11.697 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 3.89 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.976 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→59.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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