+Open data
-Basic information
Entry | Database: PDB / ID: 6cug | ||||||
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Title | Crystal structure of BC8B TCR-CD1b-PC complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / T cell receptor / antigen presenting molecule / CD1b / PC / phosphatidylcholine | ||||||
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 / positive regulation of receptor binding / early endosome lumen / 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 / 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 / early endosome membrane / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / endosome membrane / immune response / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / external side of plasma membrane / lysosomal membrane / intracellular membrane-bounded organelle / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / 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 / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Shahine, A.E. / Rossjohn, J. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: A T-cell receptor escape channel allows broad T-cell response to CD1b and membrane phospholipids. Authors: Shahine, A. / Reinink, P. / Reijneveld, J.F. / Gras, S. / Holzheimer, M. / Cheng, T.Y. / Minnaard, A.J. / Altman, J.D. / Lenz, S. / Prandi, J. / Kubler-Kielb, J. / Moody, D.B. / Rossjohn, J. / Van Rhijn, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cug.cif.gz | 338.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cug.ent.gz | 268.8 KB | Display | PDB format |
PDBx/mmJSON format | 6cug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cug_validation.pdf.gz | 836.1 KB | Display | wwPDB validaton report |
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Full document | 6cug_full_validation.pdf.gz | 845.2 KB | Display | |
Data in XML | 6cug_validation.xml.gz | 35.5 KB | Display | |
Data in CIF | 6cug_validation.cif.gz | 50.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/6cug ftp://data.pdbj.org/pub/pdb/validation_reports/cu/6cug | HTTPS FTP |
-Related structure data
Related structure data | 6cuhC 6d64C 4g8fS 4qrpS 5wl1S 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: 33530.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD1B / Plasmid: pHLSEC / Cell line (production host): 293S GnTI / Organ (production host): Kidney / Production host: Homo sapiens (human) / Strain (production host): HEK / Tissue (production host): embryonic kidney / References: UniProt: P29016 |
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#2: Protein | Mass: 11748.160 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 (production host): epithelial kidney / Cell line (production host): 293S GnTI / Organ (production host): Kidney / Production host: Homo sapiens (human) / Strain (production host): HEK / References: UniProt: P61769 |
-T-cell receptor ... , 2 types, 2 molecules DE
#3: Protein | Mass: 22726.100 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
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#4: Protein | Mass: 27598.873 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
-Sugars , 1 types, 1 molecules
#5: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 417 molecules
#6: Chemical | ChemComp-CUY / |
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#7: Chemical | ChemComp-POV / ( |
#8: Chemical | ChemComp-CL / |
#9: 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: 2.52 Å3/Da / Density % sol: 51.23 % / Description: cubic |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: PEG 3350, Tris-HCl / PH range: 7.0 - 7.4 |
-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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2017 |
Radiation | Monochromator: Channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→65.7 Å / Num. obs: 78785 / % possible obs: 100 % / Redundancy: 14.3 % / Biso Wilson estimate: 40.66 Å2 / CC1/2: 0.903 / Rpim(I) all: 0.0178 / Net I/σ(I): 5.2 |
Reflection scale | Group code: 1 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 14.4 % / Num. unique obs: 5464 / CC1/2: 0.5 / Rpim(I) all: 0.0465 / % 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: 5WL1, 4QRP, 4G8F Resolution: 2.4→54.93 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.874 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.365 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.382 / SU Rfree Blow DPI: 0.233 / SU Rfree Cruickshank DPI: 0.234
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Displacement parameters | Biso max: 106.94 Å2 / Biso mean: 32.6 Å2 / Biso min: 5.23 Å2
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Refine analyze | Luzzati coordinate error obs: 0.32 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→54.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.47 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
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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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