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- PDB-7m8t: Crystal Structure of HLA-A*11:01 in complex with NSASFSTFK, an 9-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7m8t | ||||||
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Title | Crystal Structure of HLA-A*11:01 in complex with NSASFSTFK, an 9-mer epitope from SARS-CoV-2 spike (S370-378) | ||||||
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![]() | IMMUNE SYSTEM / TCR / T cell / spike / immunology / epitope presentation | ||||||
Function / homology | ![]() 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 / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / amyloid fibril formation / Induction of Cell-Cell Fusion / 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 / learning or memory / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / Golgi membrane / focal adhesion / signaling receptor binding / 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 / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gras, S. / Nguyen, A.T. / Szeto, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: SARS-CoV-2 Spike-Derived Peptides Presented by HLA Molecules Authors: Nguyen, A.T. / Szeto, C. / Jayasinghe, D. / Lobos, C.A. / Halim, H. / Chatzileontiadou, D.S.M. / 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 | ![]() | 108.4 KB | Display | ![]() |
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PDB format | ![]() | 79.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.3 KB | Display | ![]() |
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Full document | ![]() | 463 KB | Display | |
Data in XML | ![]() | 21.1 KB | Display | |
Data in CIF | ![]() | 31.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7m8sC ![]() 7m8uC ![]() 5wjnS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32055.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 989.060 Da / Num. of mol.: 1 / Fragment: UNP residues 370-378 / Source method: obtained synthetically / Details: spike Source: (synth.) ![]() ![]() References: UniProt: P0DTC2 |
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-Non-polymers , 6 types, 455 molecules ![](data/chem/img/GOL.gif)
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#4: Chemical | ChemComp-GOL / | ||||||||
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#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-CA / | #9: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2M Ammonium Sulfate, 0.1M Calcium cacodylate pH 6.5, 0.2M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: May 6, 2020 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.5→46.72 Å / Num. obs: 67146 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 20.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.8 / Num. measured all: 458019 / Scaling rejects: 1 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5WJN Resolution: 1.5→38.41 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.079 / SU Rfree Blow DPI: 0.08 / SU Rfree Cruickshank DPI: 0.077
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Displacement parameters | Biso max: 106.4 Å2 / Biso mean: 24.56 Å2 / Biso min: 11.66 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→38.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.51 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
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