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Yorodumi- PDB-4apq: Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4apq | |||||||||
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Title | Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-sulfatide | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNITY / APC CELL SURFACE | |||||||||
Function / homology | Function and homology information regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / 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 / alpha-beta T cell receptor complex ...regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / 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 / alpha-beta T cell receptor complex / positive thymic T cell selection / positive regulation of macrophage activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-4 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / antigen processing and presentation / alpha-beta T cell activation / Generation of second messenger molecules / regulation of immune response / PD-1 signaling / cellular defense response / T cell receptor binding / positive regulation of interleukin-2 production / Neutrophil degranulation / response to bacterium / 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 / 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 / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / positive regulation of type II interferon production / sensory perception of smell / Downstream TCR signaling / late endosome / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / lysosome / early endosome / endosome membrane / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | MUS MUSCULUS (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Clarke, A.J. / Le Nours, J. / Rossjohn, J. | |||||||||
Citation | Journal: To be Published Title: Type-II Natural Killer T Cell Antigen Receptor Mediated Recognition of Cd1D-Sulfatide Authors: Patel, O. / Pellicci, D.G. / Gras, S. / Clarke, A.J. / Sandoval-Romero, M. / Le Nours, J. / Theodossis, A. / Mallevaey, T. / Gapin, L. / Cardell, S. / Godfrey, D.I. / Rossjohn, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4apq.cif.gz | 354 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4apq.ent.gz | 288.5 KB | Display | PDB format |
PDBx/mmJSON format | 4apq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4apq_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4apq_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4apq_validation.xml.gz | 30.1 KB | Display | |
Data in CIF | 4apq_validation.cif.gz | 41.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/4apq ftp://data.pdbj.org/pub/pdb/validation_reports/ap/4apq | HTTPS FTP |
-Related structure data
Related structure data | 3scmS S: Starting model for refinement |
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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: 34662.012 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 19-297 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P11609 |
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#2: Protein | Mass: 11660.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P01887 |
-MOUSE NKT TCR ... , 2 types, 2 molecules CD
#3: Protein | Mass: 22779.180 Da / Num. of mol.: 1 Fragment: MOUSE VARIABLE DOMAIN, RESIDUES 1-121, HUMAN CONSTANT DOMAIN, RESIDUES 122-212 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P01848*PLUS |
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#4: Protein | Mass: 27366.568 Da / Num. of mol.: 1 Fragment: MOUSE VARIABLE DOMAIN, RESIDUES 1-121, HUMAN CONSTANT DOMAIN, RESIDUES 122-247 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): RIL |
-Sugars , 3 types, 3 molecules
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#6: Polysaccharide | alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-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: 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 |
-Non-polymers , 2 types, 3 molecules
#8: Chemical | ChemComp-CIS / ( |
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#9: Water | ChemComp-HOH / |
-Details
Nonpolymer details | BETA-D-MANNOSE (BMA): GLYCOSYLATION FROM EXPRESSION CELL LINE ALPHA-D-MANNOSE (MAN): GLYCOSYLATION ...BETA-D-MANNOSE (BMA): GLYCOSYLAT |
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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: 3.42 Å3/Da / Density % sol: 64.01 % / Description: NONE |
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Crystal grow | pH: 6.2 / Details: 0.2M SODIUM CITRATE PH 6.2, 15% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95371 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2012 |
Radiation | Monochromator: DCM VESSEL (DOUBLE CRYSTAL MONOCHROMATOR) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95371 Å / Relative weight: 1 |
Reflection | Resolution: 3→79.6 Å / Num. obs: 27729 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Biso Wilson estimate: 95.48 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.3 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SCM Resolution: 3→36.49 Å / Cor.coef. Fo:Fc: 0.9443 / Cor.coef. Fo:Fc free: 0.9184 / SU R Cruickshank DPI: 1.113 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.287 / SU Rfree Blow DPI: 0.334 / SU Rfree Cruickshank DPI: 0.337 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 94.98 Å2
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Refine analyze | Luzzati coordinate error obs: 0.491 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→36.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.11 Å / Total num. of bins used: 14
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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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