+Open data
-Basic information
Entry | Database: PDB / ID: 5wki | |||||||||
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Title | Crystal structure of PG90 TCR-CD1b-PG complex | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / antigen presenting molecule / PG / phospholipid / MHC / CD1b / PG90 / T-cell Receptor / TCR / autoreactive | |||||||||
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 / T cell receptor complex / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding ...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 / T cell receptor complex / 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 / response to bacterium / 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 / 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 / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / 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 / Golgi apparatus / cell surface / 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 / Resolution: 2.75 Å | |||||||||
Authors | Shahine, A. / Gras, S. / Rossjohn, J. | |||||||||
Citation | Journal: Sci Immunol / Year: 2017 Title: A molecular basis of human T cell receptor autoreactivity toward self-phospholipids. Authors: Shahine, A. / Van Rhijn, I. / Cheng, T.Y. / Iwany, S. / Gras, S. / 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 | 5wki.cif.gz | 333.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wki.ent.gz | 274.2 KB | Display | PDB format |
PDBx/mmJSON format | 5wki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/5wki ftp://data.pdbj.org/pub/pdb/validation_reports/wk/5wki | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 4 types, 4 molecules ABDE
#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 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / 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 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: P61769 |
#3: Protein | Mass: 22839.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV26-1, TRA@ / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A0A087WT03, UniProt: Q6P4G7 |
#4: Protein | Mass: 27791.799 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 , 2 types, 2 molecules
#5: Polysaccharide | alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#7: Sugar | ChemComp-NAG / |
-Non-polymers , 7 types, 206 molecules
#6: Chemical | ChemComp-CUY / | ||||||||||
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#8: Chemical | ChemComp-EDO / #9: Chemical | #10: Chemical | ChemComp-D3D / ( | #11: Chemical | #12: Chemical | ChemComp-CL / | #13: 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: 2.96 Å3/Da / Density % sol: 58.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 12% PEG8K, 0.2M Zinc Acetate, 0.1M MES pH 6.2 / PH range: 5.8-6.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9753 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9753 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→75.73 Å / Num. obs: 29184 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 62.91 Å2 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.75→2.88 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 3858 / CC1/2: 0.595 / Rpim(I) all: 0.709 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→75.73 Å / Cor.coef. Fo:Fc: 0.86 / Cor.coef. Fo:Fc free: 0.83 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.081 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.925 / SU Rfree Blow DPI: 0.325 / SU Rfree Cruickshank DPI: 0.332
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Displacement parameters | Biso mean: 53.27 Å2
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Refine analyze | Luzzati coordinate error obs: 0.4 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→75.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.85 Å / Rfactor Rfree error: 0 / 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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