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Open data
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Basic information
Entry | Database: PDB / ID: 4lhu | |||||||||
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Title | Crystal Structure of 9C2 TCR bound to CD1d | |||||||||
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![]() | IMMUNE SYSTEM / NKT cells / GammaDelta TCR / CD1d / lipid recognition / PBS-44 | |||||||||
Function / homology | ![]() cellular response to stimulus / lipid antigen binding / gamma-delta T cell receptor complex / T cell selection / gamma-delta T cell activation / 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 ...cellular response to stimulus / lipid antigen binding / gamma-delta T cell receptor complex / T cell selection / gamma-delta T cell activation / 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 regulation of innate immune response / heterotypic cell-cell adhesion / small molecule binding / beta-2-microglobulin binding / detection of bacterium / positive regulation of T cell proliferation / positive regulation of phagocytosis / cell adhesion molecule binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / 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 / specific granule lumen / recycling endosome membrane / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / histone binding / T cell differentiation in thymus / protein refolding / basolateral plasma membrane / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / lysosome / endosome membrane / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Uldrich, A.P. / Le Nours, J. / Pellicci, D.G. / Gras, S. / Rossjohn, J. / Godfrey, D.I. | |||||||||
![]() | ![]() Title: CD1d-lipid antigen recognition by the gamma delta TCR. Authors: Uldrich, A.P. / Le Nours, J. / Pellicci, D.G. / Gherardin, N.A. / McPherson, K.G. / Lim, R.T. / Patel, O. / Beddoe, T. / Gras, S. / Rossjohn, J. / Godfrey, D.I. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 359.4 KB | Display | ![]() |
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PDB format | ![]() | 292 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 | ![]() | 34.4 KB | Display | |
Data in CIF | ![]() | 46.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lfhSC ![]() 2po6S 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 , 3 types, 3 molecules ABG
#1: Protein | Mass: 31758.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Protein | Mass: 28676.480 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Antibody , 1 types, 1 molecules D
#3: Antibody | Mass: 26265.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 4 types, 5 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/BMA.gif)
![](data/chem/img/BMA.gif)
#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 #7: Sugar | ChemComp-NAG / | #8: Sugar | ChemComp-BMA / | |
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-Non-polymers , 4 types, 112 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/JLS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/JLS.gif)
![](data/chem/img/CL.gif)
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#9: Chemical | ChemComp-MG / |
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#10: Chemical | ChemComp-JLS / ( |
#11: Chemical | ChemComp-CL / |
#12: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 12% PEG8000, 0.1 M Tris-HCl, pH 7.0, 0.2 M magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.869→99.692 Å / Num. all: 31239 / Num. obs: 31239 / % possible obs: 99.1 % / Redundancy: 10.9 % / Biso Wilson estimate: 92.67 Å2 / Rsym value: 0.135 |
Reflection shell | Resolution: 2.869→3.02 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2 / % possible all: 94 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 4LFH AND 2PO6 Resolution: 2.87→47.47 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.8486 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.75 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.715 / SU Rfree Blow DPI: 0.318 / SU Rfree Cruickshank DPI: 0.325
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Displacement parameters | Biso mean: 118.16 Å2
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Refine analyze | Luzzati coordinate error obs: 0.534 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.87→47.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.87→2.96 Å / Total num. of bins used: 16
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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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