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- PDB-1nez: The Crystal Structure of a TL/CD8aa Complex at 2.1A resolution:Im... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nez | ||||||
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Title | The Crystal Structure of a TL/CD8aa Complex at 2.1A resolution:Implications for Memory T cell Generation, Co-receptor Preference and Affinity | ||||||
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![]() | IMMUNE SYSTEM | ||||||
Function / homology | ![]() cytotoxic T cell differentiation / : / T cell mediated immunity / antigen processing and presentation of peptide antigen via MHC class I / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell ...cytotoxic T cell differentiation / : / T cell mediated immunity / antigen processing and presentation of peptide antigen via MHC class I / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cellular defense response / positive regulation of calcium-mediated signaling / T cell activation / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / calcium-mediated signaling / 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 / 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 / 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 / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / defense response to virus / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / receptor complex / lysosomal membrane / external side of plasma membrane / protein kinase binding / structural molecule activity / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, Y. / Xiong, Y. / Naidenko, O.V. / Liu, J.H. / Zhang, R. / Joachimiak, A. / Kronenberg, M. / Cheroutre, H. / Reinherz, E.L. / Wang, J.H. | ||||||
![]() | ![]() Title: The Crystal Structure of a TL/CD8alphaalpha Complex at 2.1 A resolution: Implications for modulation of T cell activation and memory Authors: Liu, Y. / Xiong, Y. / Naidenko, O.V. / Liu, J.H. / Zhang, R. / Joachimiak, A. / Kronenberg, M. / Cheroutre, H. / Reinherz, E.L. / Wang, J.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137 KB | Display | ![]() |
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PDB format | ![]() | 111.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 414.9 KB | Display | ![]() |
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Full document | ![]() | 437.9 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 26 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31660.002 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Mus musculus (mouse). References: UniProt: P14433, UniProt: P14432*PLUS | ||||
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#2: Protein | Mass: 11704.359 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Mus musculus (mouse). References: UniProt: P01887 | ||||
#3: Protein | Mass: 14397.548 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Mus musculus (mouse). References: UniProt: P01731 #4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.08 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.0M ammonium sulfate, 2.0% PEG 400, 5% DMSO, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 160 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.01 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 35619 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.071 / Net I/σ(I): 9.7 |
Reflection | *PLUS Num. measured all: 171093 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.18 Å / % possible obs: 100 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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