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Yorodumi- PDB-7lgd: HLA-B*07:02 in complex with SARS-CoV-2 nucleocapsid peptide N105-113 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lgd | |||||||||
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Title | HLA-B*07:02 in complex with SARS-CoV-2 nucleocapsid peptide N105-113 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / SARS-CoV-2 / HLA / T cell / cross-reactivity / COVID-19 / antigen presentation | |||||||||
Function / homology | Function and homology information cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / Maturation of nucleoprotein / regulation of interleukin-6 production / positive regulation of NLRP3 inflammasome complex assembly ...cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / Maturation of nucleoprotein / regulation of interleukin-6 production / positive regulation of NLRP3 inflammasome complex assembly / intracellular non-membrane-bounded organelle / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / TAP binding / protection from natural killer cell mediated cytotoxicity / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / RNA stem-loop binding / detection of bacterium / protein sequestering activity / 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 / secretory granule membrane / VEGFR2 mediated vascular permeability / 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 / molecular condensate scaffold activity / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / TAK1-dependent IKK and NF-kappa-B activation / cellular response to iron(III) ion / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / defense response / 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 / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / 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 / viral capsid / Interferon alpha/beta signaling / 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 / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / early endosome membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / protein refolding / host cell Golgi apparatus / viral nucleocapsid / protein homotetramerization / Translation of Structural Proteins / Virion Assembly and Release / intracellular iron ion homeostasis / host extracellular space / adaptive immune response / Induction of Cell-Cell Fusion Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.88 Å | |||||||||
Authors | Gras, S. / Szeto, C. / Chatzileontiadou, D.S.M. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Immunity / Year: 2021 Title: CD8 + T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope cross-react with selective seasonal coronaviruses. Authors: Lineburg, K.E. / Grant, E.J. / Swaminathan, S. / Chatzileontiadou, D.S.M. / Szeto, C. / Sloane, H. / Panikkar, A. / Raju, J. / Crooks, P. / Rehan, S. / Nguyen, A.T. / Lekieffre, L. / Neller, ...Authors: Lineburg, K.E. / Grant, E.J. / Swaminathan, S. / Chatzileontiadou, D.S.M. / Szeto, C. / Sloane, H. / Panikkar, A. / Raju, J. / Crooks, P. / Rehan, S. / Nguyen, A.T. / Lekieffre, L. / Neller, M.A. / Tong, Z.W.M. / Jayasinghe, D. / Chew, K.Y. / Lobos, C.A. / Halim, H. / Burrows, J.M. / Riboldi-Tunnicliffe, A. / Chen, W. / D'Orsogna, L. / Khanna, R. / Short, K.R. / Smith, C. / Gras, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lgd.cif.gz | 172.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lgd.ent.gz | 135.9 KB | Display | PDB format |
PDBx/mmJSON format | 7lgd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/7lgd ftp://data.pdbj.org/pub/pdb/validation_reports/lg/7lgd | HTTPS FTP |
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-Related structure data
Related structure data | 7lgtC 5wmnS 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 32233.285 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Escherichia coli (E. coli) / References: UniProt: P01889 #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 |
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-Protein/peptide , 1 types, 2 molecules EF
#3: Protein/peptide | Mass: 1295.464 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Severe acute respiratory syndrome coronavirus 2 References: UniProt: P0DTC9 |
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-Non-polymers , 4 types, 51 molecules
#4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-NA / | #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: 3.31 Å3/Da / Density % sol: 62.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2M Ammonium Sulfate, 0.1M HEPES pH 7.5 |
-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: 0.987 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2020 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.88→46.65 Å / Num. obs: 28141 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.898 / Rmerge(I) obs: 0.195 / Net I/σ(I): 8 / Num. measured all: 191654 / Scaling rejects: 165 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 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: 5wmn Resolution: 2.88→43.55 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.52 / Stereochemistry target values: MLHL
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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 max: 135.61 Å2 / Biso mean: 55.6076 Å2 / Biso min: 18.37 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.88→43.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.88→3.04 Å / Rfactor Rfree: 0.269 / Rfactor Rwork: 0.269 |