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- PDB-7kgr: Crystal Structure of HLA-A*0201in complex with SARS-CoV-2 N159-167 -
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Open data
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Basic information
Entry | Database: PDB / ID: 7kgr | |||||||||
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Title | Crystal Structure of HLA-A*0201in complex with SARS-CoV-2 N159-167 | |||||||||
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![]() | IMMUNE SYSTEM / HLA-A*0201 / T cell / SARS-CoV-2 / COVID-19 / viral peptide / TCR | |||||||||
Function / homology | ![]() cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / Maturation of nucleoprotein / intracellular non-membrane-bounded organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways ...cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / Maturation of nucleoprotein / intracellular non-membrane-bounded organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein sequestering activity / VEGFR2 mediated vascular permeability / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / molecular condensate scaffold activity / 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 / lumenal side of endoplasmic reticulum membrane / 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 / TAK1-dependent IKK and NF-kappa-B activation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / NOD1/2 Signaling Pathway / DDX58/IFIH1-mediated induction of interferon-alpha/beta / 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 / Interleukin-1 signaling / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / RNA stem-loop binding / 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 / Interferon alpha/beta signaling / viral capsid / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / PIP3 activates AKT signaling / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / Transcription of SARS-CoV-2 sgRNAs / iron ion transport / ER-Phagosome pathway / early endosome membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / T cell differentiation in thymus / protein refolding / host cell Golgi apparatus / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / amyloid fibril formation / Induction of Cell-Cell Fusion / Attachment and Entry / learning or memory / host cell perinuclear region of cytoplasm / ribonucleoprotein complex / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Szeto, C. / Chatzileontiadou, D.S.M. / Riboldi-Tunnicliffe, A. / Gras, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The presentation of SARS-CoV-2 peptides by the common HLA-A * 02:01 molecule. Authors: Szeto, C. / Chatzileontiadou, D.S.M. / Nguyen, A.T. / Sloane, H. / Lobos, C.A. / Jayasinghe, D. / Halim, H. / Smith, C. / Riboldi-Tunnicliffe, A. / Grant, E.J. / 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 | ![]() | 100.9 KB | Display | ![]() |
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PDB format | ![]() | 74.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.6 KB | Display | ![]() |
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Full document | ![]() | 429.6 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 26 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kgoC ![]() 7kgpC ![]() 7kgqC ![]() 7kgsC ![]() 7kgtC ![]() 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: 32153.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 970.120 Da / Num. of mol.: 1 / Fragment: residues 159-167 / Source method: obtained synthetically / Details: synthesized Source: (synth.) ![]() ![]() References: UniProt: P0DTC9 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.9 % / Mosaicity: 0.11 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20% PEG3350 w/v, 0.2 M NaFormate |
-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 6, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→48.92 Å / Num. obs: 63881 / % possible obs: 99.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 27.81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.02 / Rrim(I) all: 0.052 / Net I/σ(I): 17.5 / Num. measured all: 442231 / Scaling rejects: 9 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3GSO Resolution: 1.55→22.19 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.945 / SU R Cruickshank DPI: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.082 / SU Rfree Blow DPI: 0.08 / SU Rfree Cruickshank DPI: 0.08
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Displacement parameters | Biso max: 97.26 Å2 / Biso mean: 32.16 Å2 / Biso min: 17.6 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→22.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.56 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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