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Yorodumi- PDB-3sda: Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sda | |||||||||
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Title | Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-beta-galactosylceramide | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / CD1d / beta-linked antigen / Immunity / NKT / autoreactive | |||||||||
Function / homology | Function and homology information 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 / alpha-beta T cell activation / antigen processing and presentation / Generation of second messenger molecules / regulation of immune response / PD-1 signaling / cellular defense response / T cell receptor binding / positive regulation of interleukin-2 production / Neutrophil degranulation / 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 / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / late endosome / Downstream TCR signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / endosome membrane / early endosome / lysosome / immune response / external side of plasma membrane / lysosomal membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / 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 | Clarke, A.J. / Rossjohn, J. | |||||||||
Citation | Journal: Nat.Immunol. / Year: 2011 Title: Recognition of beta-linked self glycolipids mediated by natural killer T cell antigen receptors Authors: Pellicci, D.G. / Clarke, A.J. / Patel, O. / Mallevaey, T. / Beddoe, T. / Le Nours, J. / Uldrich, A.P. / McCluskey, J. / Besra, G.S. / Porcelli, S.A. / Gapin, L. / Godfrey, D.I. / Rossjohn, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sda.cif.gz | 177.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sda.ent.gz | 142.1 KB | Display | PDB format |
PDBx/mmJSON format | 3sda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sda_validation.pdf.gz | 979.3 KB | Display | wwPDB validaton report |
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Full document | 3sda_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3sda_validation.xml.gz | 41 KB | Display | |
Data in CIF | 3sda_validation.cif.gz | 55.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sd/3sda ftp://data.pdbj.org/pub/pdb/validation_reports/sd/3sda | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 4 types, 4 molecules ABCD
#1: Protein | Mass: 34662.012 Da / Num. of mol.: 1 / Fragment: extracellular domain, UNP residues 19-297 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1.1, Cd1d1 / Plasmid: pFastBac dual / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P11609 |
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#2: Protein | Mass: 11660.350 Da / Num. of mol.: 1 / Fragment: extracellular domain, UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pFastBac dual / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01887 |
#3: Protein | 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 Source: (gene. exp.) Mus musculus , Homo sapiens / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): RIL / References: UniProt: P01848*PLUS |
#4: Protein | Mass: 27635.912 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: chimera of Mouse variable domain and human constant domain Source: (gene. exp.) Mus musculus , Homo sapiens / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): RIL |
-Sugars , 2 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: Sugar |
-Non-polymers , 3 types, 64 molecules
#7: Chemical | ChemComp-GCY / |
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#8: Chemical | ChemComp-GOL / |
#9: Water | ChemComp-HOH / |
-Details
Sequence details | 1. SEQUENCE CONFLICT IN ENTITY 1 IS BASED ON REFERENCE 3 OF DATABASE P11609 (CD1D1_MOUSE). 2. THE ...1. SEQUENCE CONFLICT IN ENTITY 1 IS BASED ON REFERENCE 3 OF DATABASE P11609 (CD1D1_MOUSE). 2. THE SEQUENCE CONFLICT OF ENTITY 2 IS A NATURAL VARIANT ACCORDING TO DATABASE P01887 (B2MG_MOUSE). |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 0.1M Sodium Citrate, 15% PEG 6000, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 213 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.47 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 2011 |
Radiation | Monochromator: DCM vessel (double crystal monochromator) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.47 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→67.38 Å / Num. all: 32322 / Num. obs: 32322 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 76.3 Å2 / Rmerge(I) obs: 0.183 / Rsym value: 0.183 / Net I/σ(I): 6.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→65.25 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.853 / Cross valid method: THROUGHOUT / ESU R Free: 0.421 / 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: 59.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→65.25 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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