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Open data
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Basic information
Entry | Database: PDB / ID: 6xng | ||||||
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Title | MHC-like protein complex structure | ||||||
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![]() | LIPID BINDING PROTEIN / MHC-like protein / CD1d1 antigen presenting molecule / lipid binding protein complex | ||||||
Function / homology | ![]() 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 / peptide antigen binding / positive regulation of cellular senescence / 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 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thirunavukkarasu, P. / Le Nours, J. / Rossjohn, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Host immunomodulatory lipids created by symbionts from dietary amino acids. Authors: Oh, S.F. / Praveena, T. / Song, H. / Yoo, J.S. / Jung, D.J. / Erturk-Hasdemir, D. / Hwang, Y.S. / Lee, C.C. / Le Nours, J. / Kim, H. / Lee, J. / Blumberg, R.S. / Rossjohn, J. / Park, S.B. / Kasper, D.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 357.2 KB | Display | ![]() |
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PDB format | ![]() | 290.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 32.3 KB | Display | |
Data in CIF | ![]() | 45.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7m72C ![]() 6bnlS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() |
#3: Protein | Mass: 22779.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Protein | Mass: 27113.982 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Sugars , 2 types, 3 molecules
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-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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-Non-polymers , 2 types, 147 molecules ![](data/chem/img/V8P.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.57 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 18-20% PEG 3350, 8% Tacsimate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→48.56 Å / Num. obs: 29106 / % possible obs: 99.2 % / Redundancy: 9.2 % / Rpim(I) all: 0.042 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.8→2.9 Å / Num. unique obs: 4070 / Rpim(I) all: 0.283 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6BNL Resolution: 2.79→47.33 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.864 / SU R Cruickshank DPI: 1.147 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.388 / SU Rfree Blow DPI: 0.372 / SU Rfree Cruickshank DPI: 0.375
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Displacement parameters | Biso max: 152.94 Å2 / Biso mean: 73.3 Å2 / Biso min: 37.93 Å2
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Refine analyze | Luzzati coordinate error obs: 0.38 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.79→47.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.79→2.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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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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