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- PDB-3rug: Crystal structure of Valpha10-Vbeta8.1 NKT TCR in complex with CD... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3rug | |||||||||
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Title | Crystal structure of Valpha10-Vbeta8.1 NKT TCR in complex with CD1d-alphaglucosylceramide (C20:2) | |||||||||
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![]() | IMMUNE SYSTEM / mouse CD1d / mouse NKT | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Patel, O. / Rossjohn, J. | |||||||||
![]() | ![]() Title: A semi-invariant V(alpha)10(+) T cell antigen receptor defines a population of natural killer T cells with distinct glycolipid antigen-recognition properties Authors: Uldrich, A.P. / Patel, O. / Cameron, G. / Pellicci, D.G. / Day, E.B. / Sullivan, L.C. / Kyparissoudis, K. / Kjer-Nielsen, L. / Vivian, J.P. / Cao, B. / Brooks, A.G. / Williams, S.J. / ...Authors: Uldrich, A.P. / Patel, O. / Cameron, G. / Pellicci, D.G. / Day, E.B. / Sullivan, L.C. / Kyparissoudis, K. / Kjer-Nielsen, L. / Vivian, J.P. / Cao, B. / Brooks, A.G. / Williams, S.J. / Illarionov, P. / Besra, G.S. / Turner, S.J. / Porcelli, S.A. / McCluskey, J. / Smyth, M.J. / Rossjohn, J. / Godfrey, D.I. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 340.6 KB | Display | ![]() |
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PDB format | ![]() | 273.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3axlC ![]() 1z5lS ![]() 3he6S C: citing same article ( 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 3 types, 6 molecules ACBDFH
#1: Protein | Mass: 34662.012 Da / Num. of mol.: 2 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11660.350 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 27158.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Chimera of mouse variable domain and human constant domain Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Antibody , 1 types, 2 molecules EG
#3: Antibody | Mass: 22243.303 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Chimera of mouse variable domain and human constant domain Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 2 types, 6 molecules ![](data/chem/img/NAG.gif)
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 357 molecules ![](data/chem/img/DB6.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | FOR CHAIN E, G, RESIDUES 1-131 IS MOUSE VARIABLE DOMAIN AND 132-222 IS HUMAN CONSTANT DOMAIN. FOR ...FOR CHAIN E, G, RESIDUES 1-131 IS MOUSE VARIABLE DOMAIN AND 132-222 IS HUMAN CONSTANT DOMAIN. FOR CHAIN F, H, RESIDUES 1-127 IS MOUSE VARIABLE DOMAIN AND 128-257 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: 2.55 Å3/Da / Density % sol: 51.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 1500, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2010 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95453 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.2→50 Å / Num. all: 97190 / Num. obs: 97190 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.149 / Net I/σ(I): 9.2 | |||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HE6, 1Z5L Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.902 / SU B: 5.987 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.216 / 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: 23.028 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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