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- PDB-2fz3: The role of T cell receptor alpha genes in directing human MHC re... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2fz3 | ||||||
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Title | The role of T cell receptor alpha genes in directing human MHC restriction | ||||||
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![]() | IMMUNE SYSTEM / MHC / HLA-B*3508 / Ig domain | ||||||
Function / homology | ![]() host cell PML body / viral latency / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / enzyme-substrate adaptor activity / regulation of interleukin-6 production / symbiont-mediated disruption of host cell PML body / regulation of DNA replication ...host cell PML body / viral latency / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / enzyme-substrate adaptor activity / regulation of interleukin-6 production / symbiont-mediated disruption of host cell PML body / regulation of DNA replication / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / secretory granule 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 / 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 / defense response / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / 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 / 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 / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / endonuclease activity / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / DNA-binding transcription factor activity / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / innate immune response / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / positive regulation of DNA-templated transcription / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / DNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miles, J.J. / Borg, N.A. | ||||||
![]() | ![]() Title: TCR alpha genes direct MHC restriction in the potent human T cell response to a class I-bound viral epitope. Authors: Miles, J.J. / Borg, N.A. / Brennan, R.M. / Tynan, F.E. / Kjer-Nielsen, L. / Silins, S.L. / Bell, M.J. / Burrows, J.M. / McCluskey, J. / Rossjohn, J. / Burrows, S.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.3 KB | Display | ![]() |
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PDB format | ![]() | 71.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2fyyC ![]() 1zhkS C: citing same article ( S: Starting model for refinement |
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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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Details | This entry contains the crystallographic asymmetric unit which consists of 3 chains, A, B and C. |
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Components
#1: Protein | Mass: 31984.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1327.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: P03211 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 51.5 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 17% PEG 3350, 100mM cacodylate, 200mM ammonium acetate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 6, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→65.79 Å / Num. obs: 35560 / Observed criterion σ(F): 0 |
Reflection shell | Resolution: 1.9→1.949 Å / % possible all: 98.57 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1ZHK Resolution: 1.9→34.06 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.906 / SU B: 10.159 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.58 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→34.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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