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Yorodumi- PDB-1mi5: The crystal structure of LC13 TcR in complex with HLAB8-EBV pepti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mi5 | ||||||
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Title | The crystal structure of LC13 TcR in complex with HLAB8-EBV peptide complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / T cell receptor / Major histocompatability complex (class I) / HLA B8 / Epstein Barr Virus / Immunodominant TcR (LC13) | ||||||
Function / homology | Function and homology information host cell nuclear matrix / alpha-beta T cell receptor complex / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules ...host cell nuclear matrix / alpha-beta T cell receptor complex / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / 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 / viral process / secretory granule membrane / 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 / lumenal side of endoplasmic reticulum membrane / 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 / defense response / 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 / 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 / phagocytic vesicle membrane / specific granule lumen / 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 / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / Downstream TCR signaling / 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 / T cell receptor signaling pathway / 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 / endoplasmic reticulum lumen / external side of plasma membrane / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kjer-Nielsen, L. / Clements, C.S. / Purcell, A.W. / Brooks, A.G. / Whisstock, J.C. / Burrows, S.R. / McCluskey, J. / Rossjohn, J. | ||||||
Citation | Journal: IMMUNITY / Year: 2003 Title: A Structural Basis for the Selection of Dominant alphabeta T Cell Receptors in Antiviral Immunity Authors: Kjer-Nielsen, L. / Clements, C.S. / Purcell, A.W. / Brooks, A.G. / Whisstock, J.C. / Burrows, S.R. / McCluskey, J. / Rossjohn, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mi5.cif.gz | 180.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mi5.ent.gz | 142.5 KB | Display | PDB format |
PDBx/mmJSON format | 1mi5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/1mi5 ftp://data.pdbj.org/pub/pdb/validation_reports/mi/1mi5 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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 , 3 types, 3 molecules BDE
#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 |
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#4: Protein | Mass: 22317.717 Da / Num. of mol.: 1 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01848 |
#5: Protein | Mass: 27153.035 Da / Num. of mol.: 1 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01850 |
-Antibody / Protein/peptide / Non-polymers , 3 types, 234 molecules AC
#1: Antibody | Mass: 32015.055 Da / Num. of mol.: 1 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P30460, UniProt: P01889*PLUS |
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#3: Protein/peptide | Mass: 1054.247 Da / Num. of mol.: 1 / Fragment: nonamer peptide / Source method: obtained synthetically Details: Epstein barr Virus peptide was chemically synthesized. References: GenBank: 242890, UniProt: Q3KST2*PLUS |
#6: 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: 2.29 Å3/Da / Density % sol: 46.31 % | ||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG, ammonium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 7, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 29027 / Num. obs: 77349 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.5→2.6 Å / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.4 / % possible all: 95 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 29027 / Num. measured all: 77349 |
Reflection shell | *PLUS % possible obs: 95 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: the unliganded components Resolution: 2.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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