+Open data
-Basic information
Entry | Database: PDB / ID: 5swz | ||||||
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Title | Crystal Structure of NP1-B17 TCR-H2Db-NP complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / H2Db / influenza / NP366 / reversed docking / naive T cell / NP1-B17 TCR / TCR / T cell | ||||||
Function / homology | Function and homology information TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell lectin-like receptor binding ...TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell lectin-like receptor binding / natural killer cell tolerance induction / cis-Golgi network membrane / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / helical viral capsid / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / positive regulation of natural killer cell proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of immunoglobulin production / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / MHC class I protein binding / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / Neutrophil degranulation / T cell receptor binding / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / peptide binding / 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 / 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 / phagocytic vesicle membrane / peptide antigen binding / viral penetration into host nucleus / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / iron ion transport / antibacterial humoral response / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / viral nucleocapsid / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / adaptive immune response / learning or memory / early endosome / defense response to Gram-positive bacterium / immune response / symbiont entry into host cell / ribonucleoprotein complex / lysosomal membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) unidentified influenza virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å | ||||||
Authors | Gras, S. / Del Campo, C.M. / Farenc, C. / Josephs, T.M. / Rossjohn, J. | ||||||
Citation | Journal: Immunity / Year: 2016 Title: Reversed T Cell Receptor Docking on a Major Histocompatibility Class I Complex Limits Involvement in the Immune Response. Authors: Gras, S. / Chadderton, J. / Del Campo, C.M. / Farenc, C. / Wiede, F. / Josephs, T.M. / Sng, X.Y. / Mirams, M. / Watson, K.A. / Tiganis, T. / Quinn, K.M. / Rossjohn, J. / La Gruta, N.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5swz.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5swz.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 5swz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/5swz ftp://data.pdbj.org/pub/pdb/validation_reports/sw/5swz | HTTPS FTP |
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-Related structure data
Related structure data | 5swsC 1kgcS 4huuS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 4 types, 16 molecules AFKPBGLQDINSEJOT
#1: Protein | Mass: 32470.111 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01899 #2: Protein | Mass: 11660.350 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887 #4: Protein | Mass: 23117.295 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) #5: Protein | Mass: 27868.260 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
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-Protein/peptide , 1 types, 4 molecules CHMR
#3: Protein/peptide | Mass: 1026.099 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthesized / Source: (synth.) unidentified influenza virus / References: UniProt: Q9Q0U8*PLUS |
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-Non-polymers , 3 types, 543 molecules
#6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-NA / #8: Water | ChemComp-HOH / | |
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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: 2.83 Å3/Da / Density % sol: 56.49 % / Mosaicity: 0.15 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 17% 3350, 0.2 KNaTartrate, 0.1 BTP 7.5 |
-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: Jun 19, 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: 2.65→38.8 Å / Biso Wilson estimate: 66.83 Å2 |
Reflection shell | Resolution: 2.65→2.79 Å / Redundancy: 14.8 % / Rmerge(I) obs: 2.208 / Num. measured all: 272722 / Num. unique all: 18435 / CC1/2: 0.613 / Rpim(I) all: 0.013 / Rrim(I) all: 0.048 / Rsym value: 0.047 / Net I/σ(I) obs: 2 / 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: 4HUU, 1KGC Resolution: 2.65→38.8 Å / Cor.coef. Fo:Fc: 0.9015 / Cor.coef. Fo:Fc free: 0.8738 / SU R Cruickshank DPI: 0.711 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.701 / SU Rfree Blow DPI: 0.298 / SU Rfree Cruickshank DPI: 0.303
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Displacement parameters | Biso mean: 72.61 Å2
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Refine analyze | Luzzati coordinate error obs: 0.482 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→38.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.72 Å / Total num. of bins used: 20
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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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