+Open data
-Basic information
Entry | Database: PDB / ID: 3ma7 | |||||||||
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Title | Crystal structure of Cardiolipin bound to mouse CD1D | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / GAMMA DELTA T CELLS / GLYCOLIPID PRESENTATION / MHC / CD1 / CELL MEMBRANE / ENDOSOME / GLYCOPROTEIN / IMMUNE RESPONSE / IMMUNOGLOBULIN DOMAIN / INNATE IMMUNITY / LYSOSOME / MEMBRANE / TRANSMEMBRANE / MHC I / SECRETED / Disulfide bond / Immunity | |||||||||
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: 2.29 Å | |||||||||
Authors | Zajonc, D.M. | |||||||||
Citation | Journal: J.Immunol. / Year: 2011 Title: Cardiolipin Binds to CD1d and Stimulates CD1d-Restricted {gamma}{delta} T Cells in the Normal Murine Repertoire. Authors: Dieude, M. / Striegl, H. / Tyznik, A.J. / Wang, J. / Behar, S.M. / Piccirillo, C.A. / Levine, J.S. / Zajonc, D.M. / Rauch, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ma7.cif.gz | 323.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ma7.ent.gz | 261.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ma7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ma7_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 3ma7_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 3ma7_validation.xml.gz | 33.5 KB | Display | |
Data in CIF | 3ma7_validation.cif.gz | 44.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/3ma7 ftp://data.pdbj.org/pub/pdb/validation_reports/ma/3ma7 | HTTPS FTP |
-Related structure data
Related structure data | 2akrS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Refine code: 1
NCS ensembles :
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-Components
-Protein , 2 types, 4 molecules CADB
#1: Protein | Mass: 32632.668 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 19-297 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1.1, CD1D, Cd1d1 / Plasmid: PBACPHP10 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: P11609 #2: Protein | Mass: 11660.350 Da / Num. of mol.: 2 / 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: PBACPHP10 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q91XJ8, UniProt: P01887*PLUS |
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-Sugars , 2 types, 4 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / | |
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-Non-polymers , 3 types, 161 molecules
#4: Chemical | #5: 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: 2.59 Å3/Da / Density % sol: 52.5 % |
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Crystal grow | Details: 20% POLYETHYLENE GLYCOL 4000, 300MM CALCIUM ACETATE, 6% ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2007 Details: VERTICAL FOCUSING MIRROR, SINGLE CRYSTAL (SI111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING) |
Radiation | Monochromator: SIDE SCATTERING I-BEAM BENT SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→50 Å / Num. obs: 37815 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 41.8 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.29→2.38 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 1.9 / % possible all: 88.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2AKR Resolution: 2.29→44.68 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.904 / SU B: 21.736 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.407 / ESU R Free: 0.268 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.05 Å2
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Refinement step | Cycle: LAST / Resolution: 2.29→44.68 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.29→2.35 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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