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Yorodumi- PDB-2bnr: Structural and kinetic basis for heightened immunogenicity of T c... -
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-Basic information
Entry | Database: PDB / ID: 2bnr | ||||||
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Title | Structural and kinetic basis for heightened immunogenicity of T cell vaccines | ||||||
Components |
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Keywords | IMMUNE SYSTEM/RECEPTOR / IMMUNE SYSTEM-RECEPTOR-COMPLEX / TCR / MHC / IMMUNODOMINANCE / FLU / COMPLEX / TRANSMEMBRANE / GLYCOPROTEIN / POLYMORPHISM / T-CELL / RECEPTOR / SUPERAGONIST PEPTIDE T-CELL VACCINES / IMMUNE SYSTEM-RECEPTOR complex | ||||||
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 / T cell receptor complex / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation ...tRNA threonylcarbamoyladenosine metabolic process / alpha-beta T cell receptor complex / T cell mediated cytotoxicity directed against tumor cell target / T cell receptor complex / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / 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 / protection from natural killer cell mediated cytotoxicity / PD-1 signaling / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / immunoglobulin complex, circulating / immunoglobulin receptor binding / 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 / complement activation, classical pathway / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen binding / 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 / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / 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 / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / 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 / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / Downstream TCR signaling / positive regulation of T cell activation / 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 receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / blood microparticle Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Chen, J.-L. / Stewart-Jones, G. / Bossi, G. / Lissin, N.M. / Wooldridge, L. / Choi, E.M.L. / Held, G. / Dunbar, P.R. / Esnouf, R.M. / Sami, M. ...Chen, J.-L. / Stewart-Jones, G. / Bossi, G. / Lissin, N.M. / Wooldridge, L. / Choi, E.M.L. / Held, G. / Dunbar, P.R. / Esnouf, R.M. / Sami, M. / Boultier, J.M. / Rizkallah, P.J. / Renner, C. / Sewell, A. / van der Merwe, P.A. / Jackobsen, B.K. / Griffiths, G. / Jones, E.Y. / Cerundolo, V. | ||||||
Citation | Journal: J.Exp.Med. / Year: 2005 Title: Structural and Kinetic Basis for Heightened Immunogenicity of T Cell Vaccines Authors: Chen, J.-L. / Stewart-Jones, G. / Bossi, G. / Lissin, N.M. / Wooldridge, L. / Choi, E.M.L. / Held, G. / Dunbar, P.R. / Esnouf, R.M. / Sami, M. / Boultier, J.M. / Rizkallah, P. / Renner, C. / ...Authors: Chen, J.-L. / Stewart-Jones, G. / Bossi, G. / Lissin, N.M. / Wooldridge, L. / Choi, E.M.L. / Held, G. / Dunbar, P.R. / Esnouf, R.M. / Sami, M. / Boultier, J.M. / Rizkallah, P. / Renner, C. / Sewell, A. / Van Der Merwe, P.A. / Jackobsen, B.K. / Griffiths, G. / Jones, E.Y. / Cerundolo, V. #1: Journal: J.Immunol. / Year: 2000 Title: Identification of NY-Eso-1 Peptide Analogues Capable of Improved Stimulation of Tumor-Reactive Ctl Authors: Chen, J.-L. / Dunbar, P.R. / Gileadi, U. / Jager, E. / Gnjatic, S. / Nagata, Y. / Stockert, E. / Panicali, D.L. / Chen, Y.-T. / Knuth, A. / Old, L.J. / Cerundolo, V. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bnr.cif.gz | 190.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bnr.ent.gz | 149.9 KB | Display | PDB format |
PDBx/mmJSON format | 2bnr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bnr_validation.pdf.gz | 445.8 KB | Display | wwPDB validaton report |
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Full document | 2bnr_full_validation.pdf.gz | 465.5 KB | Display | |
Data in XML | 2bnr_validation.xml.gz | 37.6 KB | Display | |
Data in CIF | 2bnr_validation.cif.gz | 54.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/2bnr ftp://data.pdbj.org/pub/pdb/validation_reports/bn/2bnr | HTTPS FTP |
-Related structure data
Related structure data | 2bnqC 2bnuC 1ogaS C: citing same article (ref.) 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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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31951.316 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR ALPHA-1, -2, -3, RESIDUES 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: REFOLDED FROM INCLUSION BODIES / Cell: ANTIGEN PRESENTING CELL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR / References: UniProt: P01892, UniProt: P04439*PLUS |
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#2: Protein | Mass: 11879.356 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) Description: REFOLDED FROM INCLUSION BODIES FROM INCLUSION BODIES Cell: ANTIGEN PRESENTING CELL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR / References: UniProt: P61769 |
-T-CELL RECEPTOR ... , 2 types, 2 molecules DE
#4: Protein | Mass: 22171.480 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: CONTAINS ALSO C (CONSTANT) REGION / Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: IMMUNE SYTEM / Description: REFOLDED FROM INCLUSION BODIES / Cell: T-LYMPHOCYTE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR / References: UniProt: A0A0B4J279*PLUS |
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#5: Protein | Mass: 27005.988 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR, RESIDUES 1-130 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: IMMUNE SYTEM / Description: REFOLDED FROM INCLUSION BODIES. / Cell: T-LYMPHOCYTE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR / References: UniProt: P01850, UniProt: A0A0K0K1A5*PLUS |
-Protein/peptide / Non-polymers , 2 types, 521 molecules C
#3: Protein/peptide | Mass: 1094.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: REFOLDED FROM INCLUSION BODIES. PEPTIDE CHAIN C. / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P78358*PLUS |
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#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: 2.72 Å3/Da / Density % sol: 54.74 % |
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Crystal grow | pH: 7.2 / Details: pH 7.20 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 20, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 87826 / % possible obs: 98.5 % / Observed criterion σ(I): 0.9 / Redundancy: 11 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.5 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OGA Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 1.5
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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