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Yorodumi- PDB-3qi9: Crystal structure of mouse CD1d-alpha-phosphotidylinositol with m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qi9 | |||||||||
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Title | Crystal structure of mouse CD1d-alpha-phosphotidylinositol with mouse Valpha14-Vbeta6 2A3-D NKT TCR | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / autoreactivity / T-cell surface | |||||||||
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 / molecular replacement / Resolution: 2.3 Å | |||||||||
Authors | Clarke, A.J. / Rossjohn, J. | |||||||||
Citation | Journal: Immunity / Year: 2011 Title: A molecular basis for NKT cell recognition of CD1d-self-antigen Authors: Mallevaey, T. / Clarke, A.J. / Scott-Browne, J.P. / Young, M.H. / Roisman, L.C. / Pellicci, D.G. / Patel, O. / Vivian, J.P. / Matsuda, J.L. / McCluskey, J. / Godfrey, D.I. / Marrack, P. / ...Authors: Mallevaey, T. / Clarke, A.J. / Scott-Browne, J.P. / Young, M.H. / Roisman, L.C. / Pellicci, D.G. / Patel, O. / Vivian, J.P. / Matsuda, J.L. / McCluskey, J. / Godfrey, D.I. / Marrack, P. / Rossjohn, J. / Gapin, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qi9.cif.gz | 188.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qi9.ent.gz | 145.2 KB | Display | PDB format |
PDBx/mmJSON format | 3qi9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qi9_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3qi9_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3qi9_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 3qi9_validation.cif.gz | 48.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/3qi9 ftp://data.pdbj.org/pub/pdb/validation_reports/qi/3qi9 | HTTPS FTP |
-Related structure data
Related structure data | 3au1C 3he7S 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 , 4 types, 4 molecules ABCD
#1: Protein | Mass: 34662.012 Da / Num. of mol.: 1 / Fragment: residues in UNP 19-297 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d1, Cd1.1 / Plasmid: pFastBac Dual / Cell line (production host): Hi 5 / 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: pFastBac Dual / Cell line (production host): Hi 5 / 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 (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL |
#4: Protein | Mass: 27322.561 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 (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-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 , 4 types, 184 molecules
#7: Chemical | ChemComp-PII / | ||
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#8: Chemical | ChemComp-MG / | ||
#9: Chemical | #10: Water | ChemComp-HOH / | |
-Details
Sequence details | HIS A 201 IS FROM GENBANK DATABASE, BAB22206. ALA B 85 IS NATURAL VARIANT. |
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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: 3.44 Å3/Da / Density % sol: 64.24 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG 6000, Sodium Citrate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.47 Å |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.47 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→41 Å / Num. obs: 69852 / Redundancy: 13.3 % / Net I/σ(I): 15.3 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HE7 Resolution: 2.3→39.31 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 0 / SU B: 7.969 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.274 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
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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 max: 124.15 Å2 / Biso mean: 54.3635 Å2 / Biso min: 24.68 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→39.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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