+Open data
-Basic information
Entry | Database: PDB / ID: 3pqy | ||||||
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Title | Crystal Structure of 6218 TCR in complex with the H2Db-PA224 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / H2Db / influenza / TCR / T cell / PA epitope / repertoire / viral immunity / chimeric TCR | ||||||
Function / homology | Function and homology information 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 ...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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / positive regulation of natural killer cell mediated cytotoxicity / cap snatching / 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 / 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 / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / endonuclease activity / cellular response to lipopolysaccharide Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.192 Å | ||||||
Authors | Gras, S. / Guillonneau, C. / Turner, S.J. / Rossjohn, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Structural basis for enabling T-cell receptor diversity within biased virus-specific CD8+ T-cell responses Authors: Day, E.B. / Guillonneau, C. / Gras, S. / La Gruta, N.L. / Vignali, D.A.A. / Doherty, P.C. / Purcell, A.W. / Rossjohn, J. / Turner, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pqy.cif.gz | 645.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pqy.ent.gz | 527.8 KB | Display | PDB format |
PDBx/mmJSON format | 3pqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/3pqy ftp://data.pdbj.org/pub/pdb/validation_reports/pq/3pqy | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 2 types, 8 molecules AFKPBGLQ
#1: Protein | Mass: 32030.648 Da / Num. of mol.: 4 / Fragment: UNP residues 26-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01899 #2: Protein | Mass: 11704.359 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01887 |
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-T cell receptor ... , 2 types, 8 molecules DINSEJOT
#4: Protein | Mass: 21609.990 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: chimeric construct with mouse variable domain and human constant domain Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Gene: Trav21-dv12 / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A075B6C4, UniProt: K7N5N2 #5: Protein | Mass: 27575.906 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: chimeric construct with mouse variable domain and human constant domain Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Gene: Trbv29, B2M, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0G2LB96, UniProt: K7N5M4 |
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-Protein/peptide / Non-polymers , 2 types, 20 molecules CHMR
#3: Protein/peptide | Mass: 1186.295 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P13175*PLUS #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | SEQUENCE OF ENTITY 3 IS THE SAME AS RESIDUES 224-233 OF POLYMERASE |
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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: 2.83 Å3/Da / Density % sol: 56.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 10-14% PEG 3350, 0.2M KCN, 0.1M Bis Tris Propane pH 6.8, 5% glycerol, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.954 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 25, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 3.192→100 Å / Num. obs: 70035 / % possible obs: 97.5 % / Redundancy: 3.7 % / Rsym value: 0.096 / Net I/σ(I): 12.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1YN6 and 1KGC Resolution: 3.192→49.608 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.47 / σ(F): 1.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.468 Å2 / ksol: 0.312 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 348.23 Å2 / Biso mean: 86.9781 Å2 / Biso min: 13.31 Å2
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Refinement step | Cycle: LAST / Resolution: 3.192→49.608 Å
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