[English] 日本語
Yorodumi- PDB-6cx7: Structure of alpha-GSA[12,6P] bound by CD1d and in complex with t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cx7 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of alpha-GSA[12,6P] bound by CD1d and in complex with the Va14Vb8.2 TCR | |||||||||
Components |
| |||||||||
Keywords | IMMUNE SYSTEM / antigen-presentation / TCR / MHC-fold | |||||||||
Function / homology | Function and homology information regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / lipid antigen binding / 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 ...regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / lipid antigen binding / 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 / regulation of membrane depolarization / antigen processing and presentation / positive regulation of interleukin-4 production / regulation of immune response / cellular defense response / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / Neutrophil degranulation / cell adhesion molecule binding / T cell receptor binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / late endosome / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / histone binding / protein refolding / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / lysosome / learning or memory / early endosome / endosome membrane / defense response to Gram-positive bacterium / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Wang, J. / Zajonc, D. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2019 Title: A molecular switch in mouse CD1d modulates natural killer T cell activation by alpha-galactosylsphingamides. Authors: Wang, J. / Guillaume, J. / Janssens, J. / Remesh, S.G. / Ying, G. / Bitra, A. / Van Calenbergh, S. / Zajonc, D.M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6cx7.cif.gz | 181.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6cx7.ent.gz | 139 KB | Display | PDB format |
PDBx/mmJSON format | 6cx7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/6cx7 ftp://data.pdbj.org/pub/pdb/validation_reports/cx/6cx7 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6c5mC 6c69C 6c6aC 6c6cC 6c6eC 6c6hC 6c6jC 6cw6C 6cw9C 6cwbC 6cx5C 6cx9C 6cxaC 6cxeC 6cxfC 6ojpC 3quzS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Chimeric T cell antigen receptor ... , 2 types, 2 molecules CD
#1: Protein | Mass: 23055.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pBACpHp10 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 |
---|---|
#2: Protein | Mass: 27026.998 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pBACpHp10 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 |
-Protein , 2 types, 2 molecules AB
#3: 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, mCG_3074 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: A0A0R4J090, UniProt: P11609*PLUS |
---|---|
#4: 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: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: P01887 |
-Sugars , 2 types, 3 molecules
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#8: Sugar |
-Non-polymers , 3 types, 7 molecules
#6: Chemical | ChemComp-NA / #7: Chemical | ChemComp-PLM / | #9: Chemical | ChemComp-ELM / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.01 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 16% PEG 3350, 0.02M Citric acid, 0.08 M BIS-TRIS propane, pH 8.8 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→50 Å / Num. obs: 36299 / % possible obs: 99.5 % / Redundancy: 6 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.043 / Rrim(I) all: 0.108 / Χ2: 1.949 / Net I/σ(I): 7.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QUZ Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.744 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.489 / ESU R Free: 0.275 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 137.04 Å2 / Biso mean: 59.923 Å2 / Biso min: 33.83 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|