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Yorodumi- PDB-1z5l: Structure of a highly potent short-chain galactosyl ceramide agon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z5l | |||||||||
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Title | Structure of a highly potent short-chain galactosyl ceramide agonist bound to CD1D | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Ig fold / MHC fold | |||||||||
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 / 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 / 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 / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Zajonc, D.M. / Cantu, C. / Mattner, J. / Zhou, D. / Savage, P.B. / Bendelac, A. / Wilson, I.A. / Teyton, L. | |||||||||
Citation | Journal: Nat.Immunol. / Year: 2005 Title: Structure and function of a potent agonist for the semi-invariant natural killer T cell receptor. Authors: Zajonc, D.M. / Cantu, C. / Mattner, J. / Zhou, D. / Savage, P.B. / Bendelac, A. / Wilson, I.A. / Teyton, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z5l.cif.gz | 170.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z5l.ent.gz | 132.8 KB | Display | PDB format |
PDBx/mmJSON format | 1z5l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1z5l_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1z5l_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1z5l_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 1z5l_validation.cif.gz | 45.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/1z5l ftp://data.pdbj.org/pub/pdb/validation_reports/z5/1z5l | HTTPS FTP |
-Related structure data
Related structure data | 1cd1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | biologically active subunit is a heterodimer fomred by CD1d and beta-2-microglobulin |
-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 32632.668 Da / Num. of mol.: 2 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pRMHa3 / Cell (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: GenBank: 50333, UniProt: P11609*PLUS #2: Protein | Mass: 11660.350 Da / Num. of mol.: 2 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pRMHa3 / Cell (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: GenBank: 55153801, UniProt: P01887*PLUS |
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-Sugars , 2 types, 5 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | |
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-Non-polymers , 3 types, 169 molecules
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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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: 2.42 Å3/Da / Density % sol: 49.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: PEG 4000, calcium acetate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2004 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 48471 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rsym value: 0.075 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 2.2→2.25 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.37 / % possible all: 86.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1CD1 Resolution: 2.2→39.68 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 22.637 / SU ML: 0.256 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.249 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.352 Å2
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Refine analyze | Luzzati coordinate error obs: 0.45 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→39.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.203→2.26 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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