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Yorodumi- PDB-5yxn: A T cell receptor in complex with HLA-A0201 restricted Hepatitis ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yxn | ||||||||||||
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Title | A T cell receptor in complex with HLA-A0201 restricted Hepatitis C virus NS3 peptide (KLVALGINAV) | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / TCR-peptide-HLA complex | ||||||||||||
Function / homology | Function and homology information 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 / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / kinase binding / 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 / ER to Golgi transport vesicle membrane / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / 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 type II interferon production / peptide antigen binding / positive regulation of cellular senescence / 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 / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / nucleoside-triphosphate phosphatase / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / MHC class II protein complex binding / protein complex oligomerization / early endosome membrane / late endosome membrane / monoatomic ion channel activity / T cell receptor signaling pathway / iron ion transport / antibacterial humoral response / ER-Phagosome pathway Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Hepatitis C virus | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||||||||
Authors | Hui, F. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: To Be Published Title: Capturing HCV immune escape by targeting structural based mechanism Authors: Hui, F. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yxn.cif.gz | 187.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yxn.ent.gz | 151.5 KB | Display | PDB format |
PDBx/mmJSON format | 5yxn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yxn_validation.pdf.gz | 460.7 KB | Display | wwPDB validaton report |
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Full document | 5yxn_full_validation.pdf.gz | 477.8 KB | Display | |
Data in XML | 5yxn_validation.xml.gz | 38.4 KB | Display | |
Data in CIF | 5yxn_validation.cif.gz | 55.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/5yxn ftp://data.pdbj.org/pub/pdb/validation_reports/yx/5yxn | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-T cell receptor ... , 2 types, 2 molecules AB
#1: Protein | Mass: 21741.057 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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#2: Protein | Mass: 27456.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
-Protein , 2 types, 2 molecules CD
#3: Protein | Mass: 31854.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS |
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#4: Protein | Mass: 11819.173 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P61769*PLUS |
-Protein/peptide / Non-polymers , 2 types, 586 molecules I
#5: Protein/peptide | Mass: 998.240 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus / Production host: Escherichia coli (E. coli) / References: UniProt: P27958*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: 2.56 Å3/Da / Density % sol: 51.96 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 21% PEG 3350, 0.18 M Ammonium tartrate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9779 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9779 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→50 Å / Num. obs: 61621 / % possible obs: 99.4 % / Redundancy: 4.25 % / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.03→2.08 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.098 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.161 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: 94.22 Å2 / Biso mean: 26.045 Å2 / Biso min: 8.15 Å2
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Refinement step | Cycle: final / Resolution: 2.03→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.028→2.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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