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Yorodumi- PDB-8rlt: TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 ind... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 8rlt | ||||||
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| Title | TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 index peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / TCR-MHC / TCR / HLA-E / HBV / affinity matured / pHLA | ||||||
| Function / homology | Function and homology informationdetection 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 / negative regulation of natural killer cell mediated cytotoxicity / T cell mediated cytotoxicity directed against tumor cell target / 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 immunoglobulin production / T cell receptor complex / positive regulation of interleukin-4 production / beta-2-microglobulin binding / positive regulation of natural killer cell proliferation / 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 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / 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 / response to bacterium / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / signaling receptor activity / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / receptor ligand activity / endoplasmic reticulum lumen / Amyloid fiber formation Similarity search - Function | ||||||
| Biological species | Homo sapiens (human)![]() Hepatitis B virus | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Pengelly, R.J. / Godinho, L.F. | ||||||
| Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2024Title: 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: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 8rlt.cif.gz | 344.5 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb8rlt.ent.gz | 268.8 KB | Display | PDB format |
| PDBx/mmJSON format | 8rlt.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 8rlt_validation.pdf.gz | 504.3 KB | Display | wwPDB validaton report |
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| Full document | 8rlt_full_validation.pdf.gz | 523.1 KB | Display | |
| Data in XML | 8rlt_validation.xml.gz | 65.4 KB | Display | |
| Data in CIF | 8rlt_validation.cif.gz | 86.1 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/8rlt ftp://data.pdbj.org/pub/pdb/validation_reports/rl/8rlt | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8rluC ![]() 8rlvC C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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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.) Homo sapiens (human) / Gene: HLA-E, HLA-6.2, HLAE / Production host: ![]() #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.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: ![]() |
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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.) Homo sapiens (human) / Gene: TRAV12-2, TRA / Production host: ![]() #5: Protein | Mass: 27436.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV6-5, TRB / Production host: ![]() |
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-Protein/peptide / Non-polymers , 2 types, 248 molecules CH

| #3: Protein/peptide | Mass: 1012.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() Hepatitis B virus / References: UniProt: Q67953#6: Water | ChemComp-HOH / | |
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-Details
| Has protein modification | Y |
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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: 3.04 Å3/Da / Density % sol: 59.59 % |
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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 |
-Data collection
| Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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| Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
| 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: 2.25→79.57 Å / Num. obs: 104999 / % possible obs: 98.6 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.06 / Net I/σ(I): 10.5 |
| Reflection shell | Resolution: 2.25→2.29 Å / Rmerge(I) obs: 2.958 / Num. unique obs: 5115 / CC1/2: 0.493 / Rpim(I) all: 1.164 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→79.57 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 12.605 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.21 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: 66.902 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.25→79.57 Å
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| Refine LS restraints NCS |
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| LS refinement shell |
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About Yorodumi



Homo sapiens (human)
Hepatitis B virus
X-RAY DIFFRACTION
United Kingdom, 1items
Citation

PDBj






