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Yorodumi- PDB-8elh: Crystal Structure of HLA-B*15:01 in complex with spike derived pe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8elh | |||||||||
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Title | Crystal Structure of HLA-B*15:01 in complex with spike derived peptide NQKLIANQF from SARS-CoV-2 virus | |||||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / TCR / T cell / HLA-B*15:01 / NQK / spike / SARS-CoV-2 / COVID / immune response / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...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 / 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 / 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 / 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 / extracellular exosome / extracellular region / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | |||||||||
Authors | Murdolo, L.D. / Gras, S. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Nature / Year: 2023 Title: A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection. Authors: Augusto, D.G. / Murdolo, L.D. / Chatzileontiadou, D.S.M. / Sabatino Jr., J.J. / Yusufali, T. / Peyser, N.D. / Butcher, X. / Kizer, K. / Guthrie, K. / Murray, V.W. / Pae, V. / ...Authors: Augusto, D.G. / Murdolo, L.D. / Chatzileontiadou, D.S.M. / Sabatino Jr., J.J. / Yusufali, T. / Peyser, N.D. / Butcher, X. / Kizer, K. / Guthrie, K. / Murray, V.W. / Pae, V. / Sarvadhavabhatla, S. / Beltran, F. / Gill, G.S. / Lynch, K.L. / Yun, C. / Maguire, C.T. / Peluso, M.J. / Hoh, R. / Henrich, T.J. / Deeks, S.G. / Davidson, M. / Lu, S. / Goldberg, S.A. / Kelly, J.D. / Martin, J.N. / Vierra-Green, C.A. / Spellman, S.R. / Langton, D.J. / Dewar-Oldis, M.J. / Smith, C. / Barnard, P.J. / Lee, S. / Marcus, G.M. / Olgin, J.E. / Pletcher, M.J. / Maiers, M. / Gras, S. / Hollenbach, J.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8elh.cif.gz | 105.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8elh.ent.gz | 77 KB | Display | PDB format |
PDBx/mmJSON format | 8elh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8elh_validation.pdf.gz | 461.7 KB | Display | wwPDB validaton report |
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Full document | 8elh_full_validation.pdf.gz | 466.6 KB | Display | |
Data in XML | 8elh_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 8elh_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/8elh ftp://data.pdbj.org/pub/pdb/validation_reports/el/8elh | HTTPS FTP |
-Related structure data
Related structure data | 8elgSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32132.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) |
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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.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1076.225 Da / Num. of mol.: 1 / Fragment: NQK-OC43 peptide (UNP residues 919-927) / Source method: obtained synthetically Source: (synth.) Severe acute respiratory syndrome coronavirus 2 References: UniProt: P0DTC2 |
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-Non-polymers , 3 types, 331 molecules
#4: Chemical | ChemComp-ACT / |
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#5: Chemical | ChemComp-PEG / |
#6: Water | ChemComp-HOH / |
-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: 2.53 Å3/Da / Density % sol: 51.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2 M sodium formate, pH 7.0, 20% w/v PEG3350 |
-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: 0.956 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2022 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.956 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→45.56 Å / Num. obs: 39747 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.061 / Rrim(I) all: 0.226 / Net I/σ(I): 9.2 / Num. measured all: 535056 / Scaling rejects: 131 | ||||||||||||||||||||||||||||||
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: PDB entry 8ELG Resolution: 1.85→43.08 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.31 / Stereochemistry target values: ML
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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: 86.36 Å2 / Biso mean: 27.3839 Å2 / Biso min: 10.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→43.08 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %
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