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Yorodumi- PDB-4ftv: The complex between the high affinity version of A6 TCR (A6c134) ... -
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-Basic information
Entry | Database: PDB / ID: 4ftv | ||||||
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Title | The complex between the high affinity version of A6 TCR (A6c134) and human Class I MHC HLA-A2 with the bound TAX nonameric peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / TAX peptide / nonapeptide / MHC class I / HLA-A2 / TCR A6 / cross-reactivity / high affinity / c134 | ||||||
Function / homology | Function and homology information : / symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / 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 / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation ...: / symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / 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 / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / 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 / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / 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 / 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 / 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 / amyloid fibril formation / host cell cytoplasm / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma membrane / innate immune response / focal adhesion / signaling receptor binding / host cell nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human T-cell lymphotropic virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å | ||||||
Authors | Borbulevych, O.Y. / Baker, B.M. | ||||||
Citation | Journal: To be Published Title: Structure of a high affinity TCR reveals native binding to MHC with enhanced peptide specificity Authors: Borbulevych, O.Y. / Baker, B.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ftv.cif.gz | 347.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ftv.ent.gz | 294.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ftv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ftv_validation.pdf.gz | 479.4 KB | Display | wwPDB validaton report |
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Full document | 4ftv_full_validation.pdf.gz | 493.7 KB | Display | |
Data in XML | 4ftv_validation.xml.gz | 30.4 KB | Display | |
Data in CIF | 4ftv_validation.cif.gz | 41.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/4ftv ftp://data.pdbj.org/pub/pdb/validation_reports/ft/4ftv | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 4 types, 4 molecules ABDE
#1: Protein | Mass: 31854.203 Da / Num. of mol.: 1 / Fragment: UNP residues 25-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01892, UniProt: P04439*PLUS |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769 |
#4: Protein | Mass: 22088.162 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) / Strain (production host): BL21 |
#5: Protein | Mass: 27436.469 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) / Strain (production host): BL21 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1070.280 Da / Num. of mol.: 1 / Fragment: UNP residues 11-19 / Source method: obtained synthetically / Details: commercial Source: (synth.) Human T-cell lymphotropic virus type 1 (african isolate) References: UniProt: P0C213 |
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-Non-polymers , 2 types, 35 molecules
#6: Chemical | ChemComp-GOL / #7: 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: 2.75 Å3/Da / Density % sol: 55.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG3350 24%, MES 0.025M, NaCl 0.1M, pH 6.5, vapor diffusion, sitting drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98494 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Oct 12, 2008 |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98494 Å / Relative weight: 1 |
Reflection | Resolution: 2.74→20 Å / Num. all: 26730 / Num. obs: 26730 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.74→2.9 Å / Rmerge(I) obs: 0.557 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.2546 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8062 / SU B: 34.589 / SU ML: 0.315 / SU Rfree: 0.3771 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.377 / Stereochemistry target values: Engh & Huber / Details: U VALUES : RESIDUAL ONLY
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.64 Å2 / Biso mean: 91.077 Å2 / Biso min: 9.03 Å2
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Refinement step | Cycle: LAST / Resolution: 2.74→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.74→2.81 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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