+Open data
-Basic information
Entry | Database: PDB / ID: 4zak | |||||||||
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Title | Crystal structure of the mCD1d/DB06-1/iNKTCR ternary complex | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC-fold / Ig-fold / glycolipid antigen presentation / T cell receptor | |||||||||
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 / alpha-beta T cell receptor complex ...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 / alpha-beta T cell receptor complex / positive regulation of macrophage activation / positive thymic T cell selection / 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 / T cell receptor complex / positive regulation of interleukin-4 production / antigen processing and presentation / alpha-beta T cell activation / regulation of immune response / cellular defense response / T cell receptor binding / positive regulation of interleukin-2 production / Neutrophil degranulation / response to bacterium / 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 / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / positive regulation of type II interferon production / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / 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 / T cell receptor signaling pathway / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / early endosome / learning or memory / lysosome / endosome membrane / immune response / external side of plasma membrane / lysosomal membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.824 Å | |||||||||
Authors | Zajonc, D.M. / Birkholz, A.M. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J Immunol. / Year: 2015 Title: A Novel Glycolipid Antigen for NKT Cells That Preferentially Induces IFN-gamma Production. Authors: Birkholz, A.M. / Girardi, E. / Wingender, G. / Khurana, A. / Wang, J. / Zhao, M. / Zahner, S. / Illarionov, P.A. / Wen, X. / Li, M. / Yuan, W. / Porcelli, S.A. / Besra, G.S. / 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 | 4zak.cif.gz | 175.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zak.ent.gz | 134.1 KB | Display | PDB format |
PDBx/mmJSON format | 4zak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zak_validation.pdf.gz | 974.1 KB | Display | wwPDB validaton report |
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Full document | 4zak_full_validation.pdf.gz | 978.8 KB | Display | |
Data in XML | 4zak_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 4zak_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/4zak ftp://data.pdbj.org/pub/pdb/validation_reports/za/4zak | 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 , 4 types, 4 molecules ABCD
#1: Protein | Mass: 32632.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d1, Cd1.1 / Plasmid: pBACpHp10 / Details (production host): dual promotor / 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pBACp10pH / Details (production host): dual promotor / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P01887 |
#3: Protein | Mass: 23055.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Gene: Trav11, Trav11d, Tcr-alpha, B2M, HDCMA22P / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3), BL21DE3 References: UniProt: A0A0B4J1J9, UniProt: A0N4Z0, UniProt: K7N5M3 |
#4: Protein | Mass: 27026.998 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Plasmid: pET22b+ / Gene: Trbc2, TRBC2, TCRBC2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A0A075B5J4, UniProt: A0A5B9, UniProt: A2NTY6*PLUS |
-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 , 1 types, 1 molecules
#7: Chemical | ChemComp-4LX / |
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-Details
Has protein modification | Y |
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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 Å3/Da / Density % sol: 59.06 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% PEG 4000, 0.2M ammonium citrate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.976 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 17, 2014 |
Radiation | Monochromator: I-beam single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.824→150.76 Å / Num. all: 27210 / Num. obs: 27210 / % possible obs: 98.1 % / Redundancy: 3.9 % / Rsym value: 0.0122 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.824→2.93 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 1.9 / % possible all: 98.6 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Q7Y Resolution: 2.824→45.42 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.875 / SU B: 13.387 / SU ML: 0.259 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.318 / ESU R Free: 0.367 / 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: 99.69 Å2 / Biso mean: 48.531 Å2 / Biso min: 30.82 Å2
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Refinement step | Cycle: final / Resolution: 2.824→45.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.824→2.897 Å / Total num. of bins used: 20
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