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- PDB-6zky: Crystal structure of InhA:01 TCR in complex with HLA-E (S147C) bo... -
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Basic information
Entry | Database: PDB / ID: 6zky | ||||||||||||
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Title | Crystal structure of InhA:01 TCR in complex with HLA-E (S147C) bound to InhA (53-61 H3C) | ||||||||||||
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![]() | IMMUNE SYSTEM / T cell receptor / TCR / HLA-E / InhA | ||||||||||||
Function / homology | ![]() positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation ...positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / trans-2-enoyl-CoA reductase (NADH) activity / positive regulation of natural killer cell mediated cytotoxicity / mycolic acid biosynthetic process / positive regulation of interleukin-13 production / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / positive regulation of natural killer cell proliferation / enoyl-[acyl-carrier-protein] reductase (NADH) activity / positive regulation of immunoglobulin production / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of interleukin-4 production / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / NAD+ binding / beta-2-microglobulin binding / T cell receptor binding / negative regulation of T cell proliferation / peptidoglycan-based cell wall / 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 / fatty acid binding / 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 / 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 / positive regulation of tumor necrosis factor production / 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 / iron ion transport / antibacterial humoral response / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Srikannathasan, V. / Karuppiah, V. / Robinson, R.A. | ||||||||||||
![]() | ![]() Title: Structure-guided stabilization of pathogen-derived peptide-HLA-E complexes using non-natural amino acids conserves native TCR recognition. Authors: Barber, C. / De Souza, V.A. / Paterson, R.L. / Martin-Urdiroz, M. / Mulakkal, N.C. / Srikannathasan, V. / Connolly, M. / Phillips, G. / Foong-Leong, T. / Pengelly, R. / Karuppiah, V. / ...Authors: Barber, C. / De Souza, V.A. / Paterson, R.L. / Martin-Urdiroz, M. / Mulakkal, N.C. / Srikannathasan, V. / Connolly, M. / Phillips, G. / Foong-Leong, T. / Pengelly, R. / Karuppiah, V. / Grant, T. / Dembek, M. / Verma, A. / Gibbs-Howe, D. / Blicher, T.H. / Knox, A. / Robinson, R.A. / Cole, D.K. / Leonard, S. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 338.5 KB | Display | ![]() |
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PDB format | ![]() | 276.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6zkwC ![]() 6zkxC ![]() 6zkzC ![]() 7ndqC ![]() 7ndtC ![]() 7nduC ![]() 5eu6S ![]() 5w1wS S: Starting model for refinement C: citing same article ( |
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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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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31840.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-T-cell receptor ... , 2 types, 2 molecules DE
#4: Protein | Mass: 21496.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#5: Protein | Mass: 27491.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein/peptide / Non-polymers , 2 types, 12 molecules C![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#3: Protein/peptide | Mass: 998.285 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH) |
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#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.5 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M Sodium chloride, 0.1 M BIS-TRIS pH 6.5, 1.5 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→60.08 Å / Num. obs: 27789 / % possible obs: 99.75 % / Redundancy: 15 % / CC1/2: 0.999 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.037 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.65→2.7 Å / Redundancy: 14.1 % / Rmerge(I) obs: 2.442 / Mean I/σ(I) obs: 1 / Num. unique obs: 1288 / CC1/2: 0.615 / Rpim(I) all: 0.657 / % possible all: 95.76 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5w1w, 5eu6 Resolution: 2.65→60.08 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 45.874 / SU ML: 0.389 / Cross valid method: THROUGHOUT / ESU R: 2.489 / ESU R Free: 0.366 / 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: 78.825 Å2
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Refinement step | Cycle: 1 / Resolution: 2.65→60.08 Å
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