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Yorodumi- PDB-3o4l: Genetic and structural basis for selection of a ubiquitous T cell... -
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-Basic information
Entry | Database: PDB / ID: 3o4l | ||||||
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Title | Genetic and structural basis for selection of a ubiquitous T cell receptor deployed in Epstein-Barr virus | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC I / Immunoglobulin / Antigen Presentation / Immune Recognition | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / alpha-beta T cell receptor complex / 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 / mRNA transport / positive regulation of ferrous iron binding ...symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / alpha-beta T cell receptor complex / 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 / mRNA transport / 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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / 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 / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / sensory perception of smell / Downstream TCR signaling / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / host cell cytoplasm / 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 / focal adhesion / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / Neutrophil degranulation / regulation of DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / identical protein binding / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human herpesvirus 4 (Epstein-Barr virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.54 Å | ||||||
Authors | Miles, J.J. / Bulek, A.M. / Cole, D.K. / Gostick, E. / Schauenburg, J.A. / Dolton, G. / Venturi, V. / Davenport, M.P. / Tan, M.P. / Burrows, S.R. ...Miles, J.J. / Bulek, A.M. / Cole, D.K. / Gostick, E. / Schauenburg, J.A. / Dolton, G. / Venturi, V. / Davenport, M.P. / Tan, M.P. / Burrows, S.R. / Wooldridge, L. / Price, D.A. / Rizkallah, P.J. / Sewell, A.K. | ||||||
Citation | Journal: Plos Pathog. / Year: 2010 Title: Genetic and structural basis for selection of a ubiquitous T cell receptor deployed in Epstein-Barr virus infection. Authors: Miles, J.J. / Bulek, A.M. / Cole, D.K. / Gostick, E. / Schauenburg, A.J. / Dolton, G. / Venturi, V. / Davenport, M.P. / Tan, M.P. / Burrows, S.R. / Wooldridge, L. / Price, D.A. / Rizkallah, P.J. / Sewell, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o4l.cif.gz | 358.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o4l.ent.gz | 289.9 KB | Display | PDB format |
PDBx/mmJSON format | 3o4l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/3o4l ftp://data.pdbj.org/pub/pdb/validation_reports/o4/3o4l | HTTPS FTP |
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-Related structure data
Related structure data | 2p5eS 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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Details | The contents of the asymmetric unit constitute one complete biological assembly. |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31951.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WLS4 |
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#2: Protein | Mass: 11853.319 Da / Num. of mol.: 1 / Mutation: K111C / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61769 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 920.191 Da / Num. of mol.: 1 / Fragment: residues 286-294 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 4 (Epstein-Barr virus) / References: UniProt: A7UMS0, UniProt: Q3KSU1*PLUS |
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-T-CELL RECEPTOR, ... , 2 types, 2 molecules DE
#4: Protein | Mass: 21960.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01848*PLUS |
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#5: Protein | Mass: 27412.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01850*PLUS |
-Non-polymers , 4 types, 353 molecules
#6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-SO4 / #8: Chemical | ChemComp-MES / | #9: 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: 2.52 Å3/Da / Density % sol: 51.23 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.16 M Ca Acetate, 0.08 M Na Cacodylate, 12.5% PEG 8000, 20% Glycerol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.54→61.25 Å / Num. all: 31817 / Num. obs: 31817 / % possible obs: 99.1 % / Redundancy: 7.9 % / Rsym value: 0.163 / Net I/σ(I): 12.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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Phasing MR | R rigid body: 0.479 / Cor.coef. Fo:Fc: 0.497 / Cor.coef. Io to Ic: 0.52 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2P5E Resolution: 2.54→61.25 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.833 / WRfactor Rfree: 0.261 / WRfactor Rwork: 0.1936 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7883 / SU B: 27.238 / SU ML: 0.274 / SU R Cruickshank DPI: 0.2811 / SU Rfree: 0.3704 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100 Å2 / Biso mean: 27.6561 Å2 / Biso min: 4.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.54→61.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.54→2.606 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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