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- PDB-8rlv: TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 L6I... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8rlv | ||||||
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Title | TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 L6I peptide | ||||||
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![]() | IMMUNE SYSTEM / TCR-MHC / TCR / HLA-E / HBV / affinity matured / pHLA | ||||||
Function / homology | ![]() detection of tumor cell / 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 lectin-like receptor binding / natural killer cell tolerance induction ...detection of tumor cell / 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 lectin-like receptor binding / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / caveolin-mediated endocytosis of virus by host cell / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / alpha-beta T cell receptor complex / positive regulation of natural killer cell proliferation / negative regulation of natural killer cell mediated cytotoxicity / T cell mediated cytotoxicity directed against tumor cell target / 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 / T cell receptor complex / positive regulation of interleukin-4 production / beta-2-microglobulin binding / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / 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 / T cell receptor binding / negative regulation of T cell proliferation / : / : / 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 / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / antibacterial humoral response / late endosome membrane / sensory perception of smell / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / signaling receptor activity / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / early endosome membrane / protein refolding / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pengelly, R.J. / Godinho, L.F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Viral sequence determines HLA-E-restricted T cell recognition of hepatitis B surface antigen. Authors: Murugesan, G. / Paterson, R.L. / Kulkarni, R. / Ilkow, V. / Suckling, R.J. / Connolly, M.M. / Karuppiah, V. / Pengelly, R. / Jadhav, A. / Donoso, J. / Heunis, T. / Bunjobpol, W. / Philips, G. ...Authors: Murugesan, G. / Paterson, R.L. / Kulkarni, R. / Ilkow, V. / Suckling, R.J. / Connolly, M.M. / Karuppiah, V. / Pengelly, R. / Jadhav, A. / Donoso, J. / Heunis, T. / Bunjobpol, W. / Philips, G. / Ololade, K. / Kay, D. / Sarkar, A. / Barber, C. / Raj, R. / Perot, C. / Grant, T. / Treveil, A. / Walker, A. / Dembek, M. / Gibbs-Howe, D. / Hock, M. / Carreira, R.J. / Atkin, K.E. / Dorrell, L. / Knox, A. / Leonard, S. / Salio, M. / Godinho, L.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 628 KB | Display | ![]() |
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PDB format | ![]() | 506.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 502.8 KB | Display | ![]() |
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Full document | ![]() | 521.3 KB | Display | |
Data in XML | ![]() | 65.4 KB | Display | |
Data in CIF | ![]() | 84.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8rltC ![]() 8rluC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Refine code: 1 / Auth asym-ID: A / Label asym-ID: A
NCS ensembles :
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Components
-Protein , 2 types, 4 molecules AFBG
#1: Protein | Mass: 31824.008 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-T cell receptor ... , 2 types, 4 molecules DIEJ
#4: Protein | Mass: 21944.373 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #5: Protein | Mass: 27436.559 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, 132 molecules CH

#3: Protein/peptide | Mass: 1012.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #6: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% (w/v) PEG 3350, 100 mM BIS-TRIS propane pH 8.5, 200 mM sodium sulfate Collection Temp: 100 |
-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: Feb 14, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.609→79.65 Å / Num. obs: 67783 / % possible obs: 99.2 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.057 / Net I/σ(I): 0.142 |
Reflection shell | Resolution: 2.609→2.65 Å / Rmerge(I) obs: 3.246 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 3323 / CC1/2: 0.313 / Rpim(I) all: 1.345 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 94.35 Å2
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Refinement step | Cycle: LAST / Resolution: 2.609→79.65 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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