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Yorodumi- PDB-3arb: Ternary crystal structure of the NKT TCR-CD1d-alpha-galactosylcer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3arb | |||||||||
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Title | Ternary crystal structure of the NKT TCR-CD1d-alpha-galactosylceramide analogue-OCH | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / mouse NKT TCR / mouse CD1d | |||||||||
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 / peptide antigen assembly with MHC class I protein complex / 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 / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Wun, K.S. / Rossjohn, J. | |||||||||
Citation | Journal: Immunity / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3arb.cif.gz | 354.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3arb.ent.gz | 286.6 KB | Display | PDB format |
PDBx/mmJSON format | 3arb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/3arb ftp://data.pdbj.org/pub/pdb/validation_reports/ar/3arb | HTTPS FTP |
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-Related structure data
Related structure data | 3ardC 3areC 3arfC 3argC 3he6S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 34662.012 Da / Num. of mol.: 1 / Fragment: heavy chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d1, Cd1.1 / Plasmid: pBacP10PH / Production host: Trichoplusia ni (cabbage looper) / 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 / Plasmid: pBacP10PH / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01887 |
#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.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: P01850*PLUS |
-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.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: P01848*PLUS |
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-Sugars , 2 types, 4 molecules
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / | |
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-Non-polymers , 4 types, 72 molecules
#6: Chemical | #8: Chemical | ChemComp-FEE / | #9: Chemical | ChemComp-D12 / | #10: Water | ChemComp-HOH / | |
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-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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 61.01 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 22% 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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95453 Å | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2010 | |||||||||||||||||||||
Radiation | Monochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95453 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. all: 34141 / Num. obs: 32741 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 68 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 9.3 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HE6 Resolution: 2.7→48.84 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.89 / SU B: 29.468 / SU ML: 0.268 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.333 / 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: 56.06 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→48.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 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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