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- PDB-3arg: Ternary crystal structure of the mouse NKT TCR-CD1d-alpha-glucosy... -
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Basic information
Entry | Database: PDB / ID: 3arg | |||||||||
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Title | Ternary crystal structure of the mouse NKT TCR-CD1d-alpha-glucosylceramide(C20:2) | |||||||||
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![]() | IMMUNE SYSTEM / mouse NKT TCR / mouse CD1d | |||||||||
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 / alpha-beta T cell receptor complex ...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 / 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 / positive regulation of interleukin-4 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / antigen processing and presentation / alpha-beta T cell activation / Generation of second messenger molecules / regulation of immune response / PD-1 signaling / cellular defense response / T cell receptor binding / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of interleukin-2 production / Neutrophil degranulation / complement activation, classical pathway / 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 / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / positive regulation of type II interferon production / sensory perception of smell / late endosome / Downstream TCR signaling / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / 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 / lysosome / early endosome / blood microparticle / endosome membrane / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wun, K.S. / Rossjohn, J. | |||||||||
![]() | ![]() Title: A molecular basis for the exquisite CD1d-restricted antigen specificity and functional responses of natural killer T cells Authors: Wun, K.S. / Cameron, G. / Patel, O. / Pang, S.S. / Pellicci, D.G. / Sullivan, L.C. / Keshipeddy, S. / Young, M.H. / Uldrich, A.P. / Thakur, M.S. / Richardson, S.K. / Howell, A.R. / ...Authors: Wun, K.S. / Cameron, G. / Patel, O. / Pang, S.S. / Pellicci, D.G. / Sullivan, L.C. / Keshipeddy, S. / Young, M.H. / Uldrich, A.P. / Thakur, M.S. / Richardson, S.K. / Howell, A.R. / Illarionov, P.A. / Brooks, A.G. / Besra, G.S. / McCluskey, J. / Gapin, L. / Porcelli, S.A. / Godfrey, D.I. / Rossjohn, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 337.1 KB | Display | ![]() |
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PDB format | ![]() | 270.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 30.5 KB | Display | |
Data in CIF | ![]() | 41.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3arbC ![]() 3ardC ![]() 3areC ![]() 3arfC ![]() 3he6S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 3 types, 3 molecules ABD
#1: Protein | Mass: 34662.012 Da / Num. of mol.: 1 / Fragment: heavy chain 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: 27166.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Chimera of mouse variable domain and human constant domain,Chimera of mouse variable domain and human constant domain Source: (gene. exp.) ![]() ![]() ![]() Plasmid: pET / Production host: ![]() ![]() |
-Antibody , 1 types, 1 molecules C
#3: Antibody | Mass: 22779.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Chimera of mouse variable domain and human constant domain,Chimera of mouse variable domain and human constant domain Source: (gene. exp.) ![]() ![]() ![]() Plasmid: pET / Production host: ![]() ![]() |
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-Sugars , 2 types, 3 molecules ![](data/chem/img/NAG.gif)
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / | |
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-Non-polymers , 2 types, 23 molecules ![](data/chem/img/DB6.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-DB6 / ( |
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#8: Water | ChemComp-HOH / |
-Details
Sequence details | FOR CHAIN C, RESIDUES 1 TO 116 IS MOUSE VARIABLE DOMAIN AND 117-210 IS HUMAN CONSTANT DOMAIN. FOR ...FOR CHAIN C, RESIDUES 1 TO 116 IS MOUSE VARIABLE DOMAIN AND 117-210 IS HUMAN CONSTANT DOMAIN. FOR CHAIN D, RESIDUES 1 TO 117 IS MOUSE VARIABLE DOMAIN AND 118-247 IS HUMAN CONSTANT DOMAIN. THE SWISS-PROT ENTRY P11609 CONFLICTS WITH BRADBURY ET AL., 1988 WHICH SUGGESTS A HISTIDINE IN PLACE OF ASPARTATE. SEQUENCE IN THIS PDB AGREES WITH THE CITATION. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.75 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20% PEG 400, 0.1M Ammonium acetate, 0.1M Bis Tris, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2009 | |||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95367 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. all: 24965 / Num. obs: 23592 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 61.1 Å2 / Rmerge(I) obs: 0.218 / Net I/σ(I): 9.4 | |||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HE6 Resolution: 3→47.56 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.854 / SU B: 55.794 / SU ML: 0.446 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.491 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.513 Å2
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Refinement step | Cycle: LAST / Resolution: 3→47.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.996→3.074 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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