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Yorodumi- PDB-7ejl: Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-2)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ejl | ||||||
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Title | Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-2) spike protein | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA-A*2402 / MHC CLASS I / coronavirus | ||||||
Function / homology | Function and homology information 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 / 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 ...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 / 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 / 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 / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / 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 / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / 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 / 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 / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / signaling receptor binding / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Murayama, K. / Kato-Murayama, M. / Shirouzu, M. | ||||||
Citation | Journal: Commun Biol / Year: 2021 Title: Identification of TCR repertoires in functionally competent cytotoxic T cells cross-reactive to SARS-CoV-2. Authors: Shimizu, K. / Iyoda, T. / Sanpei, A. / Nakazato, H. / Okada, M. / Ueda, S. / Kato-Murayama, M. / Murayama, K. / Shirouzu, M. / Harada, N. / Hidaka, M. / Fujii, S.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ejl.cif.gz | 124.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ejl.ent.gz | 75.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ejl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ejl_validation.pdf.gz | 441.7 KB | Display | wwPDB validaton report |
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Full document | 7ejl_full_validation.pdf.gz | 442.5 KB | Display | |
Data in XML | 7ejl_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 7ejl_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/7ejl ftp://data.pdbj.org/pub/pdb/validation_reports/ej/7ejl | HTTPS FTP |
-Related structure data
Related structure data | 7ejmC 7ejnC 4f7mS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32071.357 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Details (production host): Cell-free protein synthesis / Production host: Escherichia coli (E. coli) / References: UniProt: A0A411J078 |
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#2: Protein | Mass: 12267.627 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Details (production host): Cell-free protein synthesis / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1297.521 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Severe acute respiratory syndrome coronavirus 2 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: Na/K phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jan 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→45.89 Å / Num. obs: 80351 / % possible obs: 98.73 % / Redundancy: 7.8 % / Biso Wilson estimate: 27.95 Å2 / CC1/2: 0.996 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.89→1.96 Å / Num. unique obs: 7913 / CC1/2: 0.483 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4F7M Resolution: 1.89→45.69 Å / SU ML: 0.3582 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.9837 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→45.69 Å
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Refine LS restraints |
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LS refinement shell |
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