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- PDB-7rtd: SARS-CoV-2 Spike-derived peptide S269-277 (YLQPRTFLL) presented b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rtd | ||||||
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Title | SARS-CoV-2 Spike-derived peptide S269-277 (YLQPRTFLL) presented by HLA-A*02:01 | ||||||
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![]() | IMMUNE SYSTEM / human leukocyte antigen / major histocompatibility complex / HLA-A2 / HLA-A*02:01 / YLQPRTFLL | ||||||
Function / homology | ![]() antigen processing and presentation / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway ...antigen processing and presentation / 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 / 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 / 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 / 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 / sensory perception of smell / 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 / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / amyloid fibril formation / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / learning or memory / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / immune response / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / external side of plasma membrane / lysosomal membrane / fusion of virus membrane with host plasma membrane / focal adhesion / fusion of virus membrane with host endosome membrane / viral envelope / Neutrophil degranulation / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / host cell plasma membrane / virion membrane / cell surface / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Szeto, C. / Nguyen, A.T. / Gras, S. | ||||||
Funding support | 1items
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![]() | ![]() Title: Molecular Basis of a Dominant SARS-CoV-2 Spike-Derived Epitope Presented by HLA-A*02:01 Recognised by a Public TCR. Authors: Szeto, C. / Nguyen, A.T. / Lobos, C.A. / Chatzileontiadou, D.S.M. / Jayasinghe, D. / Grant, E.J. / Riboldi-Tunnicliffe, A. / Smith, C. / Gras, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.6 KB | Display | ![]() |
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PDB format | ![]() | 76 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7rtrC ![]() 3gsoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 40974.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: Q53Z42 |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1151.377 Da / Num. of mol.: 1 / Fragment: epitope YLQPRTFLL (UNP residues 269-277) / Source method: obtained synthetically Source: (synth.) ![]() ![]() References: UniProt: P0DTC2 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M NaFluoride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 18, 2020 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.05→47.43 Å / Num. obs: 27701 / % possible obs: 97.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 32.47 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.067 / Rrim(I) all: 0.122 / Net I/σ(I): 8.6 / Num. measured all: 92488 / Scaling rejects: 57 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.4 %
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3GSO Resolution: 2.05→40.06 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.208 / SU Rfree Blow DPI: 0.172 / SU Rfree Cruickshank DPI: 0.173
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Displacement parameters | Biso max: 93.67 Å2 / Biso mean: 29.22 Å2 / Biso min: 12.31 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.05→40.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.06 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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