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Yorodumi- PDB-2axg: The Immunogenicity of a Viral Cytotoxic T Cell Epitope is control... -
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-Basic information
Entry | Database: PDB / ID: 2axg | ||||||
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Title | The Immunogenicity of a Viral Cytotoxic T Cell Epitope is controlled by its MHC-bound Conformation | ||||||
Components |
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Keywords | IMMUNE SYSTEM/GENE REGULATION / immune response / pMHC / IMMUNE SYSTEM-GENE REGULATION COMPLEX | ||||||
Function / homology | Function and homology information symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / release from viral latency / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / TAP binding / protection from natural killer cell mediated cytotoxicity ...symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / release from viral latency / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / secretory granule membrane / 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 / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / defense response / 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 / Interferon alpha/beta signaling / 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 / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / sequence-specific DNA binding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / protein dimerization activity / immune response / DNA-binding transcription factor activity / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / external side of plasma membrane / lysosomal membrane / innate immune response / focal adhesion / signaling receptor binding / virus-mediated perturbation of host defense response / host cell nucleus / Neutrophil degranulation / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / Golgi apparatus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Tynan, F.E. / Elhassen, D. / Purcell, A.W. / Burrows, J.M. / Borg, N.A. / Miles, J.J. / Williamson, N.A. / Green, K.J. / Tellam, J. / Kjer-Nielsen, L. ...Tynan, F.E. / Elhassen, D. / Purcell, A.W. / Burrows, J.M. / Borg, N.A. / Miles, J.J. / Williamson, N.A. / Green, K.J. / Tellam, J. / Kjer-Nielsen, L. / McCluskey, J. / Rossjohn, J. / Burrows, S.R. | ||||||
Citation | Journal: J.Exp.Med. / Year: 2005 Title: The immunogenicity of a viral cytotoxic T cell epitope is controlled by its MHC-bound conformation Authors: Tynan, F.E. / Elhassen, D. / Purcell, A.W. / Burrows, J.M. / Borg, N.A. / Miles, J.J. / Williamson, N.A. / Green, K.J. / Tellam, J. / Kjer-Nielsen, L. / McCluskey, J. / Rossjohn, J. / Burrows, S.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2axg.cif.gz | 95.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2axg.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 2axg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2axg_validation.pdf.gz | 456.5 KB | Display | wwPDB validaton report |
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Full document | 2axg_full_validation.pdf.gz | 463.4 KB | Display | |
Data in XML | 2axg_validation.xml.gz | 21 KB | Display | |
Data in CIF | 2axg_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/2axg ftp://data.pdbj.org/pub/pdb/validation_reports/ax/2axg | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31940.246 Da / Num. of mol.: 1 / Fragment: residues 1-276 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30685, UniProt: P01889*PLUS | ||
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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) / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769 | ||
#3: Protein/peptide | Mass: 1057.112 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Synthetic Peptide APQPAPENAY from BZLF1 protein of Epstein Barr Virus References: UniProt: P03206 | ||
#4: Chemical | #5: 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: 2.55 Å3/Da / Density % sol: 51.84 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 200mM Ammonium Acetate, 17% W/V PEG 3350, 100mM Cacodylate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 21, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 28293 |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 82.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / σ(F): 0
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Displacement parameters | Biso mean: 31.974 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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