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Yorodumi- PDB-3dxa: Crystal Structure of the DM1 TCR in complex with HLA-B*4405 and d... -
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Basic information
| Entry | Database: PDB / ID: 3dxa | ||||||
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| Title | Crystal Structure of the DM1 TCR in complex with HLA-B*4405 and decamer EBV antigen | ||||||
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Keywords | IMMUNE SYSTEM / MHC / Glycoprotein / Glycation / Host-virus interaction / Immune response / Membrane / MHC I / Transmembrane / Pyrrolidone carboxylic acid / Disease mutation | ||||||
| Function / homology | Function and homology informationhost cell nuclear matrix / viral latency / symbiont-mediated perturbation of host apoptosis / regulation of interleukin-12 production / regulation of dendritic cell differentiation / alpha-beta T cell receptor complex / regulation of T cell anergy / regulation of interleukin-6 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains ...host cell nuclear matrix / viral latency / symbiont-mediated perturbation of host apoptosis / regulation of interleukin-12 production / regulation of dendritic cell differentiation / alpha-beta T cell receptor complex / regulation of T cell anergy / regulation of interleukin-6 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / TAP binding / alpha-beta T cell activation / protection from natural killer cell mediated cytotoxicity / Generation of second messenger molecules / Co-inhibition by PD-1 / 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 / detection of bacterium / secretory granule membrane / 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 / response to bacterium / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / defense response / 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 / 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 / tertiary granule lumen / Downstream TCR signaling / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space Similarity search - Function | ||||||
| Biological species | Homo sapiens (human) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å | ||||||
Authors | Archbold, J.K. / Macdonald, W.A. / Gras, S. / Rossjohn, J. | ||||||
Citation | Journal: J.Exp.Med. / Year: 2009Title: Natural micropolymorphism in human leukocyte antigens provides a basis for genetic control of antigen recognition. Authors: Archbold, J.K. / Macdonald, W.A. / Gras, S. / Ely, L.K. / Miles, J.J. / Bell, M.J. / Brennan, R.M. / Beddoe, T. / Wilce, M.C. / Clements, C.S. / Purcell, A.W. / McCluskey, J. / Burrows, S.R. / Rossjohn, J. | ||||||
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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 | 3dxa.cif.gz | 472.8 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb3dxa.ent.gz | 384.2 KB | Display | PDB format |
| PDBx/mmJSON format | 3dxa.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 3dxa_validation.pdf.gz | 528.1 KB | Display | wwPDB validaton report |
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| Full document | 3dxa_full_validation.pdf.gz | 602.9 KB | Display | |
| Data in XML | 3dxa_validation.xml.gz | 86.3 KB | Display | |
| Data in CIF | 3dxa_validation.cif.gz | 117.2 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/3dxa ftp://data.pdbj.org/pub/pdb/validation_reports/dx/3dxa | HTTPS FTP |
-Related structure data
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Assembly
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1
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Homo sapiens (human)
X-RAY DIFFRACTION
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