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Yorodumi- PDB-6c09: Ternary crystal structure of the 3C8 TCR-CD1c-monoacylglycerol complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c09 | |||||||||
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Title | Ternary crystal structure of the 3C8 TCR-CD1c-monoacylglycerol complex | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / T cell Receptor / Antigen Presentation | |||||||||
Function / homology | Function and homology information glycolipid binding / T cell activation involved in immune response / 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 / positive regulation of receptor binding ...glycolipid binding / T cell activation involved in immune response / 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 / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / 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 / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / 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 / peptide antigen binding / positive regulation of cellular senescence / 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 / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / 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 / external side of plasma membrane / Golgi membrane / lysosomal membrane / intracellular membrane-bounded organelle / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | |||||||||
Authors | Wun, K.S. / Rossjohn, J. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Nat. Immunol. / Year: 2018 Title: T cell autoreactivity directed toward CD1c itself rather than toward carried self lipids. Authors: Wun, K.S. / Reijneveld, J.F. / Cheng, T.Y. / Ladell, K. / Uldrich, A.P. / Le Nours, J. / Miners, K.L. / McLaren, J.E. / Grant, E.J. / Haigh, O.L. / Watkins, T.S. / Suliman, S. / Iwany, S. / ...Authors: Wun, K.S. / Reijneveld, J.F. / Cheng, T.Y. / Ladell, K. / Uldrich, A.P. / Le Nours, J. / Miners, K.L. / McLaren, J.E. / Grant, E.J. / Haigh, O.L. / Watkins, T.S. / Suliman, S. / Iwany, S. / Jimenez, J. / Calderon, R. / Tamara, K.L. / Leon, S.R. / Murray, M.B. / Mayfield, J.A. / Altman, J.D. / Purcell, A.W. / Miles, J.J. / Godfrey, D.I. / Gras, S. / Price, D.A. / Van Rhijn, I. / 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 | 6c09.cif.gz | 338.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c09.ent.gz | 272.6 KB | Display | PDB format |
PDBx/mmJSON format | 6c09.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/6c09 ftp://data.pdbj.org/pub/pdb/validation_reports/c0/6c09 | HTTPS FTP |
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-Related structure data
Related structure data | 6c15C 1bd2S 3ov6S 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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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32283.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD1C / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P29017 |
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#2: Protein | Mass: 12646.157 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P61769 |
-3C8 T cell receptor ... , 2 types, 2 molecules CD
#3: Protein | Mass: 22947.650 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria) |
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#4: Protein | Mass: 27587.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria) |
-Sugars , 1 types, 1 molecules
#5: Sugar | ChemComp-NAG / |
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-Non-polymers , 6 types, 23 molecules
#6: Chemical | ChemComp-EKG / ( | ||||||||
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#7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-PEG / | #11: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG 3350, 0.2M potassium thiocynate |
-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: Jul 31, 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: 2.95→80 Å / Num. obs: 30233 / % possible obs: 100 % / Redundancy: 7.8 % / Biso Wilson estimate: 99.46 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.07 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.95→3.11 Å / Redundancy: 8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4343 / CC1/2: 0.15 / Rpim(I) all: 0.76 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OV6, 1BD2 Resolution: 2.95→37.53 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.56 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.503 / SU Rfree Blow DPI: 0.269 / SU Rfree Cruickshank DPI: 0.278
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Displacement parameters | Biso mean: 92.29 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.95→37.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.05 Å / Total num. of bins used: 15
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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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