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Yorodumi- PDB-7tlt: SARS-CoV-2 Spike-derived peptide S489-497 (YFPLQSYGF) presented b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tlt | ||||||
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Title | SARS-CoV-2 Spike-derived peptide S489-497 (YFPLQSYGF) presented by HLA-A*29:02 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / human leukocyte antigen / major histocompatibility complex / HLA-A29 / HLA-A*29:02 / SARS-CoV-2 / Spike | ||||||
Function / homology | Function and homology information : / 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 ...: / 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 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 / Attachment and Entry / membrane fusion / 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 / fusion of virus membrane with host plasma membrane / lysosomal 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 / host cell plasma membrane / structural molecule activity / virion membrane / cell surface / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Murdolo, L.D. / Szeto, C. / Gras, S. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Ablation of CD8 + T cell recognition of an immunodominant epitope in SARS-CoV-2 Omicron variants BA.1, BA.2 and BA.3. Authors: Swaminathan, S. / Lineburg, K.E. / Panikkar, A. / Raju, J. / Murdolo, L.D. / Szeto, C. / Crooks, P. / Le Texier, L. / Rehan, S. / Dewar-Oldis, M.J. / Barnard, P.J. / Ambalathingal, G.R. / ...Authors: Swaminathan, S. / Lineburg, K.E. / Panikkar, A. / Raju, J. / Murdolo, L.D. / Szeto, C. / Crooks, P. / Le Texier, L. / Rehan, S. / Dewar-Oldis, M.J. / Barnard, P.J. / Ambalathingal, G.R. / Neller, M.A. / Short, K.R. / Gras, S. / Khanna, R. / Smith, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tlt.cif.gz | 174.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tlt.ent.gz | 133.9 KB | Display | PDB format |
PDBx/mmJSON format | 7tlt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tlt_validation.pdf.gz | 475.1 KB | Display | wwPDB validaton report |
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Full document | 7tlt_full_validation.pdf.gz | 479.2 KB | Display | |
Data in XML | 7tlt_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 7tlt_validation.cif.gz | 37.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/7tlt ftp://data.pdbj.org/pub/pdb/validation_reports/tl/7tlt | HTTPS FTP |
-Related structure data
Related structure data | 7jyvS 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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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 40888.672 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLA Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: B0UXQ0 #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: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P61769 |
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-Protein/peptide , 1 types, 2 molecules EF
#3: Protein/peptide | Mass: 1121.241 Da / Num. of mol.: 2 / Fragment: UNP residues 489-497 (YFPLQSYGF) / Source method: obtained synthetically Source: (synth.) Severe acute respiratory syndrome coronavirus 2 References: UniProt: P0DTC2 |
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-Non-polymers , 4 types, 39 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | #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: 2.31 Å3/Da / Density % sol: 41.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1.9 M Ammonium Sulfate, 20 mM Magnesium chloride, 0.1M Bis-tris propane, 2% Ethylene glycol, 2% 2-Methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953739 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 5, 2021 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.953739 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.3→48.22 Å / Num. obs: 37380 / % possible obs: 95.4 % / Redundancy: 2 % / Biso Wilson estimate: 40.65 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.074 / Rrim(I) all: 0.112 / Net I/σ(I): 4.1 / Num. measured all: 75049 / Scaling rejects: 45 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 2.1 %
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7JYV Resolution: 2.3→41.29 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.887 / SU R Cruickshank DPI: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.296 / SU Rfree Blow DPI: 0.219 / SU Rfree Cruickshank DPI: 0.229
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Displacement parameters | Biso max: 138.14 Å2 / Biso mean: 48.68 Å2 / Biso min: 24.57 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→41.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.32 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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