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- PDB-5yxu: an affinity enhanced T cell receptor in complex with HLA-A0201 re... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yxu | ||||||||||||
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Title | an affinity enhanced T cell receptor in complex with HLA-A0201 restricted HCV NS3 peptide KLVALGINAV | ||||||||||||
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![]() | IMMUNE SYSTEM / affinity enhanced TCR-pHLA complex | ||||||||||||
Function / homology | ![]() positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation ...positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / T cell mediated cytotoxicity directed against tumor cell target / 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 / host cell mitochondrial membrane / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / host cell lipid droplet / CD8 receptor binding / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / positive regulation of cytokinesis / antigen processing and presentation of exogenous peptide antigen via MHC class I / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / negative regulation of protein secretion / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / 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 / 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 / kinase binding / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / SH3 domain binding / 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 / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / nucleoside-triphosphate phosphatase / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / protein complex oligomerization / late endosome membrane / monoatomic ion channel activity / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() | ||||||||||||
![]() | Yi, L. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: an affinity enhanced T cell receptor in complex with HLA-A0201 restricted HCV NS3 peptide KLVALGINAV Authors: Yi, L. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 332.2 KB | Display | ![]() |
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PDB format | ![]() | 275.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 504.6 KB | Display | ![]() |
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Full document | ![]() | 556.9 KB | Display | |
Data in XML | ![]() | 63.3 KB | Display | |
Data in CIF | ![]() | 86.4 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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2 | ![]()
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Unit cell |
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Components
-T cell receptor ... , 2 types, 4 molecules FAGB
#1: Protein | Mass: 21630.986 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 27424.521 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Protein , 2 types, 4 molecules CEDH
#3: Protein | Mass: 31925.281 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 11819.173 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Protein/peptide / Non-polymers , 2 types, 184 molecules IJ![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Protein/peptide | Mass: 998.240 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 15% PEG 3350, 0.2M potassium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å |
Detector | Type: OXFORD RUBY CCD / Detector: CCD / Date: Jun 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 48316 / % possible obs: 99.5 % / Redundancy: 3.02 % / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.7→2.85 Å |
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Processing
Software |
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Refinement | Resolution: 2.7→17.7 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.807 / SU B: 18.62 / SU ML: 0.376 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.418 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 102.25 Å2 / Biso mean: 29.975 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: final / Resolution: 2.7→17.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.768 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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