+Open data
-Basic information
Entry | Database: PDB / ID: 5l2k | ||||||
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Title | Crystal structure of GEM42 TCR-CD1b-GMM complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / CD1b / lipid / TB / MTb / GMM / tuberculosis / GEM T cell / TCR / T cell / GEM42 | ||||||
Function / homology | Function and homology information 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 ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression ...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 ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / 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 / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / endosome membrane / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / intracellular membrane-bounded organelle / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å | ||||||
Authors | Gras, S. / Shahine, A. / Le Nours, J. / Rossjohn, J. | ||||||
Citation | Journal: Nat Commun / Year: 2016 Title: T cell receptor recognition of CD1b presenting a mycobacterial glycolipid. Authors: Gras, S. / Van Rhijn, I. / Shahine, A. / Cheng, T.Y. / Bhati, M. / Tan, L.L. / Halim, H. / Tuttle, K.D. / Gapin, L. / Le Nours, J. / Moody, D.B. / Rossjohn, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l2k.cif.gz | 182.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l2k.ent.gz | 139.6 KB | Display | PDB format |
PDBx/mmJSON format | 5l2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/5l2k ftp://data.pdbj.org/pub/pdb/validation_reports/l2/5l2k | HTTPS FTP |
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-Related structure data
Related structure data | 5l2jSC 4g8fS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 4 types, 4 molecules ABDE
#1: Protein | Mass: 33488.609 Da / Num. of mol.: 1 / Mutation: I160A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD1B / Plasmid: pHLsec / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P29016 |
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#2: Protein | Mass: 11616.964 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pHLsec / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P61769 |
#3: Protein | Mass: 22646.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
#4: Protein | Mass: 27312.568 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
-Sugars , 1 types, 3 molecules
#5: Sugar |
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-Non-polymers , 7 types, 20 molecules
#6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-CL / #8: Chemical | #9: Chemical | ChemComp-6UL / | #10: Chemical | ChemComp-CS / | #11: Chemical | ChemComp-70E / | #12: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | Ligand 70E, C36 GLUCOSE MONOMYCOLATE, was built with R chirality at C5, as it best fits the density ...Ligand 70E, C36 GLUCOSE MONOMYCOLA |
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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: 4.09 Å3/Da / Density % sol: 69.93 % / Mosaicity: 0.16 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.5-2M NH4SO4, 0.1M Tris-HCl pH8.5, 10mM MgCl2, 10mM CeCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→47.73 Å / Biso Wilson estimate: 78.5 Å2 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 61.1 % / Rmerge(I) obs: 7.76 / Num. measured all: 227748 / Num. unique all: 3727 / CC1/2: 0.638 / Rpim(I) all: 0.011 / Rrim(I) all: 0.083 / Rsym value: 0.082 / Net I/σ(I) obs: 1.8 / Rejects: 0 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5L2J, 4G8F Resolution: 3.2→47.73 Å / Cor.coef. Fo:Fc: 0.9075 / Cor.coef. Fo:Fc free: 0.898 / SU R Cruickshank DPI: 8.754 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.376 / SU Rfree Cruickshank DPI: 0.381
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Displacement parameters | Biso mean: 80.56 Å2
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Refine analyze | Luzzati coordinate error obs: 0.704 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→47.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.33 Å / Total num. of bins used: 13
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