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Yorodumi- PDB-3g08: Crystal structure of the alpha-galactosylceramide analog OCH in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g08 | |||||||||
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Title | Crystal structure of the alpha-galactosylceramide analog OCH in complex with mouse CD1d | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / antigen presentation / glycolipid / NKT cells / Cell membrane / Endosome / Glycoprotein / Immune response / Immunoglobulin domain / Innate immunity / Lysosome / Membrane / Transmembrane / MHC I / Secreted | |||||||||
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 / 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 / positive regulation of immune response / positive regulation of type II interferon production / sensory perception of smell / late endosome / positive regulation of T cell activation / 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 / lysosome / early endosome / endosome membrane / immune response / lysosomal membrane / external side of plasma 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: 1.6 Å | |||||||||
Authors | Zajonc, D.M. | |||||||||
Citation | Journal: J.Immunol. / Year: 2010 Title: Mechanisms for glycolipid antigen-driven cytokine polarization by Valpha14i NKT cells. Authors: Sullivan, B.A. / Nagarajan, N.A. / Wingender, G. / Wang, J. / Scott, I. / Tsuji, M. / Franck, R.W. / Porcelli, S.A. / Zajonc, D.M. / Kronenberg, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g08.cif.gz | 190.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g08.ent.gz | 149.3 KB | Display | PDB format |
PDBx/mmJSON format | 3g08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g08_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3g08_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3g08_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 3g08_validation.cif.gz | 32.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/3g08 ftp://data.pdbj.org/pub/pdb/validation_reports/g0/3g08 | HTTPS FTP |
-Related structure data
Related structure data | 2q7yS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32632.668 Da / Num. of mol.: 1 / Fragment: UNP residues 19-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1.1, CD1d, Cd1d1 / Plasmid: pBACp10pH / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P11609 |
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#2: Protein | Mass: 11660.350 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) Gene: B2m, beta 2 microglobulin, mCG_11606, RP23-34E24.5-001 Plasmid: pBACp10pH / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q91XJ8, UniProt: P01887*PLUS |
-Sugars , 2 types, 3 molecules
#3: 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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#4: Sugar |
-Non-polymers , 3 types, 479 molecules
#5: Chemical | ChemComp-FEE / |
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#6: Chemical | ChemComp-PLM / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.95 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 16% polyethylene glycol 3350, 100mM Tris pH8.5, 2% tacsimate pH8.0 , VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97976 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 10, 2009 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing) |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97976 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→29.67 Å / Num. all: 65322 / Num. obs: 63903 / % possible obs: 97.82 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 2.6 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2Q7Y Resolution: 1.6→29.67 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.66 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.087 / 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: 24.464 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→29.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.637 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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