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Yorodumi- PDB-1zhk: Crystal structure of HLA-B*3501 presenting 13-mer EBV antigen LPE... -
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-Basic information
Entry | Database: PDB / ID: 1zhk | ||||||
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Title | Crystal structure of HLA-B*3501 presenting 13-mer EBV antigen LPEPLPQGQLTAY | ||||||
Components |
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Keywords | IMMUNE SYSTEM / T-cell receptor / bulged epitopes | ||||||
Function / homology | Function and homology information regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / 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 / detection of bacterium / secretory granule membrane ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / 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 / 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 / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / 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 / peptide antigen assembly with MHC class I protein complex / 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 / defense response / 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 / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / 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 / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / 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 / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / 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: 1.6 Å | ||||||
Authors | Tynan, F.E. / Borg, N.A. / Miles, J.J. / Beddoe, T. / El-Hassen, D. / Silins, S.L. / van Zuylen, W.J. / Purcell, A.W. / Kjer-Nielsen, L. / McCluskey, J. ...Tynan, F.E. / Borg, N.A. / Miles, J.J. / Beddoe, T. / El-Hassen, D. / Silins, S.L. / van Zuylen, W.J. / Purcell, A.W. / Kjer-Nielsen, L. / McCluskey, J. / Burrows, S.R. / Rossjohn, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: The high resolution structures of highly bulged viral epitopes bound to the major histocompatability class I: Implications for T-cell receptor engagement and T-cell immunodominance Authors: Tynan, F.E. / Borg, N.A. / Miles, J.J. / Beddoe, T. / El-Hassen, D. / Silins, S.L. / van Zuylen, W.J. / Purcell, A.W. / Kjer-Nielsen, L. / McCluskey, J. / Burrows, S.R. / Rossjohn, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zhk.cif.gz | 97.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zhk.ent.gz | 78.8 KB | Display | PDB format |
PDBx/mmJSON format | 1zhk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/1zhk ftp://data.pdbj.org/pub/pdb/validation_reports/zh/1zhk | 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
#1: Protein | Mass: 31940.246 Da / Num. of mol.: 1 / Fragment: Extracellular domains alpha 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: 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: 1426.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide LPEPLPQGQLTAY |
#4: 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: 2.7 Å3/Da / Density % sol: 53.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 0.2M Ammonium Acetate, 17% w/v PEG 3350, 100mM Cacodylate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.54179 Å |
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Detector | Date: Nov 25, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 60254 / % possible obs: 96.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.07 / % possible all: 84 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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