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Yorodumi- PDB-3dxa: Crystal Structure of the DM1 TCR in complex with HLA-B*4405 and d... -
+Open data
-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 | ||||||
Components |
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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 information host cell nuclear matrix / viral latency / symbiont-mediated perturbation of host apoptosis / alpha-beta T cell receptor complex / regulation of interleukin-12 production / regulation of dendritic cell differentiation / 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 / alpha-beta T cell receptor complex / regulation of interleukin-12 production / regulation of dendritic cell differentiation / 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 / alpha-beta T cell activation / TAP binding / Generation of second messenger molecules / protection from natural killer cell mediated cytotoxicity / PD-1 signaling / detection of bacterium / secretory granule membrane / 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 / 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 / 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 / defense response / 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 / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / Downstream TCR signaling / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / early endosome membrane / late endosome membrane / T cell receptor signaling pathway / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / external side of plasma membrane / lysosomal membrane / innate immune response / focal adhesion / signaling receptor binding / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface 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: 2009 Title: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dxa.cif.gz | 468.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dxa.ent.gz | 393.3 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
-Links
-Assembly
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1
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