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Yorodumi- PDB-5m02: Crystal structure of murine P14 TCR / H-2Db with PF, modified gp3... -
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-Basic information
Entry | Database: PDB / ID: 5m02 | ||||||
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Title | Crystal structure of murine P14 TCR / H-2Db with PF, modified gp33 peptide from LCMV | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC class I / TCR / H-2Db / gp33 / LCMV | ||||||
Function / homology | Function and homology information Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / Downstream TCR signaling / alpha-beta T cell receptor complex / TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity ...Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / Downstream TCR signaling / alpha-beta T cell receptor complex / 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 tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / cis-Golgi network membrane / positive regulation of natural killer cell activation / 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 / T cell receptor complex / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / positive regulation of natural killer cell proliferation / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / positive regulation of immunoglobulin production / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / negative regulation of T cell proliferation / 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 / Neutrophil degranulation / T cell receptor binding / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / response to bacterium / 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 / 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 / phagocytic vesicle membrane / peptide antigen binding / 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 / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / signaling receptor activity / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Lymphocytic choriomeningitis virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Achour, A. / Sandalova, T. / Sun, R. | ||||||
Citation | Journal: To Be Published Title: Thernary complexes of TCR P14 give insights into the mechanisms behind reestablishment of CTL responses against a viral escape mutant Authors: Allerbring, E. / Duru, A. / Sun, R. / Han, X. / Uchtenhagen, H. / Madhurantakam, C. / Popov, A. / Markova, N. / Talyzina, A. / Nygren, P.A. / Sandalova, T. / Achour, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m02.cif.gz | 344.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m02.ent.gz | 279 KB | Display | PDB format |
PDBx/mmJSON format | 5m02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/5m02 ftp://data.pdbj.org/pub/pdb/validation_reports/m0/5m02 | HTTPS FTP |
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-Related structure data
Related structure data | 5m00C 5m01C 5tjeC 1s7uS S: Starting model for refinement C: citing same article (ref.) |
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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 , 4 types, 4 molecules ABGH
#1: Protein | Mass: 32087.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899 |
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#2: Protein | Mass: 13794.978 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887 |
#3: Protein | Mass: 23072.697 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trav14-1, Tcra / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G2JF94, UniProt: P01849 |
#4: Protein | Mass: 26647.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P04213, UniProt: P01851 |
-Protein/peptide , 1 types, 1 molecules P
#5: Protein/peptide | Mass: 1027.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: KAPFNFATM / Source: (synth.) Lymphocytic choriomeningitis virus |
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-Non-polymers , 2 types, 395 molecules
#6: Chemical | #7: 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: 2.75 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 19% PEG 6000, 0.1M Tris HCl pH 8.0 / PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→128 Å / Num. obs: 103816 / % possible obs: 98.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 5042 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1s7u Resolution: 1.75→127.14 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.736 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.395 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→127.14 Å
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