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Yorodumi- PDB-2p5w: Crystal structures of high affinity human T-cell receptors bound ... -
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-Basic information
Entry | Database: PDB / ID: 2p5w | ||||||
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Title | Crystal structures of high affinity human T-cell receptors bound to pMHC reveal native diagonal binding geometry | ||||||
Components |
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Keywords | IMMUNE SYSTEM / T-CELL RECEPTOR / CDR2 / PHAGE DISPLAY / MUTANT / HIGH AFFINITY / NY-ESO-1 | ||||||
Function / homology | Function and homology information tRNA threonylcarbamoyladenosine metabolic process / alpha-beta T cell receptor complex / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding ...tRNA threonylcarbamoyladenosine metabolic process / alpha-beta T cell receptor complex / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / alpha-beta T cell activation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / Generation of second messenger molecules / TAP binding / PD-1 signaling / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / detection of bacterium / T cell receptor binding / 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 / 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 / response to bacterium / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / 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 / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / positive regulation of type II interferon production / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / Downstream TCR signaling / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / T cell receptor signaling pathway / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / antibacterial humoral response / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Sami, M. / Rizkallah, P.J. / Dunn, S. / Li, Y. / Moysey, R. / Vuidepot, A. / Baston, E. / Todorov, P. / Molloy, P. / Gao, F. ...Sami, M. / Rizkallah, P.J. / Dunn, S. / Li, Y. / Moysey, R. / Vuidepot, A. / Baston, E. / Todorov, P. / Molloy, P. / Gao, F. / Boulter, J.M. / Jakobsen, B.K. | ||||||
Citation | Journal: Protein Eng.Des.Sel. / Year: 2007 Title: Crystal structures of high affinity human T-cell receptors bound to peptide major histocompatibility complex reveal native diagonal binding geometry Authors: Sami, M. / Rizkallah, P.J. / Dunn, S. / Molloy, P. / Moysey, R. / Vuidepot, A. / Baston, E. / Todorov, P. / Yi, L. / Gao, F. / Boulter, J.M. / Jakobsen, B.K. | ||||||
History |
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Remark 999 | Sequence No suitable database reference was found for Chains D and E at time of processing |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p5w.cif.gz | 201.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p5w.ent.gz | 156.8 KB | Display | PDB format |
PDBx/mmJSON format | 2p5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/2p5w ftp://data.pdbj.org/pub/pdb/validation_reports/p5/2p5w | HTTPS FTP |
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-Related structure data
Related structure data | 2p5eC 2pyeC 2pyfC 2f53S 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 ABDE
#1: Protein | Mass: 31951.316 Da / Num. of mol.: 1 Fragment: EXTRACELLULAR DOMAINS ALPHA 1, ALPHA2 AND ALPHA3, RESIDUES 25-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: PEX078 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01892, UniProt: P04439*PLUS |
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#2: Protein | Mass: 11853.319 Da / Num. of mol.: 1 / Fragment: Beta-2 Microglobulin, RESIDUES 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: PEX050 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P61769 |
#4: Protein | Mass: 21073.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGMT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6PIZ8, UniProt: P01848*PLUS |
#5: Protein | Mass: 27367.514 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGMT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q2YDB4 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1094.347 Da / Num. of mol.: 1 / Fragment: RESIDUES 157-165 / Source method: obtained synthetically Details: THIS SEQUENCE OCCURS NATURALLY IN HOMO SAPIENS (HUMANS) References: UniProt: P78358 |
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-Non-polymers , 6 types, 695 molecules
#6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-GOL / #8: Chemical | ChemComp-CA / | #9: Chemical | ChemComp-MG / | #10: Chemical | ChemComp-EPE / | #11: 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: 2.46 Å3/Da / Density % sol: 50.04 % |
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Crystal grow | Temperature: 293 K / pH: 7.5 Details: 85 MM HEPES, 8.5% ISO-PROPANOL, 17% PEG4000, 15% GLYCEROL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.985 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 2004 / Details: MIRROR |
Radiation | Monochromator: SI (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.985 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→24.805 Å / Num. obs: 46229 / % possible obs: 99.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.145 / Rsym value: 0.145 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.51 / % possible all: 99.5 |
-Phasing
Phasing MR | Rfactor: 0.438 / Cor.coef. Fo:Fc: 0.527 / Cor.coef. Io to Ic: 0.491
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2F53 Resolution: 2.2→24.8 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.912 / SU B: 12.038 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.825 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→24.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 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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