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Yorodumi- PDB-4mx7: Structure of mouse CD1d in complex with dioleoyl-phosphatidic acid -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mx7 | |||||||||
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Title | Structure of mouse CD1d in complex with dioleoyl-phosphatidic acid | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC fold / antigen presentation / lipid antigen / membrane | |||||||||
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: 2.24 Å | |||||||||
Authors | Zajonc, D.M. / Wang, J. | |||||||||
Citation | Journal: To be Published Title: TBN Authors: Wang, J. / Zajonc, D.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mx7.cif.gz | 169.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mx7.ent.gz | 133.3 KB | Display | PDB format |
PDBx/mmJSON format | 4mx7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mx7_validation.pdf.gz | 933.5 KB | Display | wwPDB validaton report |
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Full document | 4mx7_full_validation.pdf.gz | 943.9 KB | Display | |
Data in XML | 4mx7_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 4mx7_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/4mx7 ftp://data.pdbj.org/pub/pdb/validation_reports/mx/4mx7 | 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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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32609.609 Da / Num. of mol.: 1 / Fragment: CD1d ectdomain, UNP residues 19-297 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1.1, Cd1d1, mcd1d / Plasmid: pBACpHp10 transfer vector / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 cells / References: UniProt: P11609 |
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#2: Protein | Mass: 11660.350 Da / Num. of mol.: 1 / Fragment: b2M ectodomain, UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pBACpHp10 transfer vector / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 cells / References: UniProt: P01887 |
-Sugars , 2 types, 3 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
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#4: Sugar |
-Non-polymers , 2 types, 116 molecules
#5: Chemical | ChemComp-MX7 / ( |
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#6: 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: 2.72 Å3/Da / Density % sol: 54.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 20% PEG 4000, 0.2M ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 29, 2013 |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→75.58 Å / Num. all: 23912 / Num. obs: 23843 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.24→2.37 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3414 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2Q7Y Resolution: 2.24→75.58 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.896 / SU B: 13.083 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 27.478 Å2
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Refinement step | Cycle: LAST / Resolution: 2.24→75.58 Å
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