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Yorodumi- PDB-8qfy: Crystal structure of high affinity TCR in complex with pHLA harbo... -
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-Basic information
Entry | Database: PDB / ID: 8qfy | ||||||
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Title | Crystal structure of high affinity TCR in complex with pHLA harbouring bacterial peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / T-cell receptor / HLA-E | ||||||
Function / homology | Function and homology information 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 / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell proliferation / 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 / beta-2-microglobulin binding / T cell receptor binding / negative regulation of T cell proliferation / 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 / 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 / lumenal side of endoplasmic reticulum membrane / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of tumor necrosis factor production / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / antibacterial humoral response / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Pengelly, R.J. / Robinson, R.A. | ||||||
Funding support | 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024 Title: An HLA-E-targeted TCR bispecific molecule redirects T cell immunity against Mycobacterium tuberculosis. Authors: Paterson, R.L. / La Manna, M.P. / Arena De Souza, V. / Walker, A. / Gibbs-Howe, D. / Kulkarni, R. / Fergusson, J.R. / Mulakkal, N.C. / Monteiro, M. / Bunjobpol, W. / Dembek, M. / Martin- ...Authors: Paterson, R.L. / La Manna, M.P. / Arena De Souza, V. / Walker, A. / Gibbs-Howe, D. / Kulkarni, R. / Fergusson, J.R. / Mulakkal, N.C. / Monteiro, M. / Bunjobpol, W. / Dembek, M. / Martin-Urdiroz, M. / Grant, T. / Barber, C. / Garay-Baquero, D.J. / Tezera, L.B. / Lowne, D. / Britton-Rivet, C. / Pengelly, R. / Chepisiuk, N. / Singh, P.K. / Woon, A.P. / Powlesland, A.S. / McCully, M.L. / Caccamo, N. / Salio, M. / Badami, G.D. / Dorrell, L. / Knox, A. / Robinson, R. / Elkington, P. / Dieli, F. / Lepore, M. / Leonard, S. / Godinho, L.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qfy.cif.gz | 350.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qfy.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8qfy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/8qfy ftp://data.pdbj.org/pub/pdb/validation_reports/qf/8qfy | HTTPS FTP |
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-Related structure data
Related structure data | 4ww2S 6gh1S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-Protein , 2 types, 4 molecules AAAFFFBBBGGG
#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: Escherichia coli (E. coli) / References: UniProt: P13747 #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 |
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-Protein/peptide , 1 types, 2 molecules CCCHHH
#3: Protein/peptide | Mass: 980.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria) |
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-T-cell receptor ... , 2 types, 4 molecules DDDIIIEEEJJJ
#4: Protein | Mass: 22079.363 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #5: Protein | Mass: 27693.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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-Non-polymers , 2 types, 283 molecules
#6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 3.57 Å3/Da / Density % sol: 65.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M calcium acetate, 0.1 M imidazole pH 8.0, 10% PEG 8000 |
-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 X 16M / Detector: PIXEL / Date: Sep 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→82.9 Å / Num. obs: 114168 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.987 / Rmerge(I) obs: 0.121 / Rrim(I) all: 0.131 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.33→2.37 Å / Redundancy: 6 % / Rmerge(I) obs: 3.209 / Num. unique obs: 5720 / CC1/2: 0.34 / Rrim(I) all: 3.521 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GH1, 4WW2 Resolution: 2.33→82.9 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.253 / WRfactor Rwork: 0.206 / SU B: 15.989 / SU ML: 0.323 / Average fsc free: 0.6939 / Average fsc work: 0.7064 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.238 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: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.978 Å2
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Refinement step | Cycle: LAST / Resolution: 2.33→82.9 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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