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- PDB-7sis: SARS-CoV-2 Spike-derived peptide S976-984 (VLNDILSRL) presented b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7sis | ||||||
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Title | SARS-CoV-2 Spike-derived peptide S976-984 (VLNDILSRL) presented by HLA-A*02:01 | ||||||
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![]() | IMMUNE SYSTEM / human leukocyte antigen / major histocompatibility complex / HLA-A2 / HLA-A*02:01 / SARS-CoV-2 / Spike / VLNDILSRL | ||||||
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 / lumenal side of endoplasmic reticulum membrane ...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 / 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 / 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 / external side of plasma membrane / fusion of virus membrane with host 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 Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Szeto, C. / Gras, S. | ||||||
Funding support | 1items
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![]() | ![]() Title: The impact of SARS-CoV-2 spike mutation on peptide presentation is HLA allomorph-specific Authors: Szeto, 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 | ![]() | 104.7 KB | Display | ![]() |
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PDB format | ![]() | 76.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.6 KB | Display | ![]() |
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Full document | ![]() | 449.3 KB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 29 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ogaS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 32038.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: Q861F7 |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: P61769 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1043.239 Da / Num. of mol.: 1 / Fragment: UNP residues 976-984 / Source method: obtained synthetically Source: (synth.) ![]() ![]() References: UniProt: P0DTC2 |
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-Non-polymers , 4 types, 357 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CD.gif)
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#4: Chemical | ChemComp-ACT / |
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#5: Chemical | ChemComp-CD / |
#6: Chemical | ChemComp-ZN / |
#7: 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: 3.01 Å3/Da / Density % sol: 59.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 20% PEG 3350, 0.2M Ammonium Formate, 1 mM CdCl2 |
-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: Jul 14, 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: 1.9→48.33 Å / Num. obs: 42888 / % possible obs: 99.3 % / Redundancy: 8.5 % / Biso Wilson estimate: 32.58 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.039 / Rrim(I) all: 0.115 / Net I/σ(I): 11.7 / Num. measured all: 365840 / Scaling rejects: 34 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1OGA Resolution: 1.9→45.66 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.122 / SU Rfree Blow DPI: 0.117 / SU Rfree Cruickshank DPI: 0.113
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Displacement parameters | Biso max: 116.79 Å2 / Biso mean: 37.09 Å2 / Biso min: 8.47 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→45.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.92 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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