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Yorodumi- PDB-7lg3: Human leukocyte antigen A*0201 in complex with SARS-CoV2 epitope ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lg3 | ||||||
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Title | Human leukocyte antigen A*0201 in complex with SARS-CoV2 epitope KLWAQCVQL | ||||||
Components |
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Keywords | IMMUNE SYSTEM/VIRAL PROTEIN / SARS-CoV2 / CD8+ / epitope / HLA / human major histocompatibility complex / MHC-I / KLWAQCVQL / HLA-A2 / HLA-A*02:01 / IMMUNE SYSTEM-VIRAL PROTEIN 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 / 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 / lumenal side of endoplasmic reticulum membrane / 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 / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / peptide antigen binding / positive regulation of cellular senescence / 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 / positive regulation of T cell activation / sensory perception of smell / protein guanylyltransferase activity / negative regulation of neuron projection development / RNA endonuclease activity, producing 3'-phosphomonoesters / positive regulation of protein binding / tertiary granule lumen / mRNA guanylyltransferase activity / DAP12 signaling / 5'-3' RNA helicase activity / MHC class II protein complex binding / late endosome membrane / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / snRNP Assembly / iron ion transport / ER-Phagosome pathway / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / host cell endosome / early endosome membrane / symbiont-mediated suppression of host toll-like receptor signaling pathway / T cell differentiation in thymus / symbiont-mediated degradation of host mRNA / protein refolding / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / protein homotetramerization / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / intracellular iron ion homeostasis / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / amyloid fibril formation / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Patskovska, L. / Patskovsky, Y. / Krogsgaard, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Human leukocyte antigen A*0201 in complex with SARS-CoV2 epitope KLWAQCVQL Authors: Patskovska, L. / Patskovsky, Y. / Krogsgaard, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lg3.cif.gz | 176.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lg3.ent.gz | 138.4 KB | Display | PDB format |
PDBx/mmJSON format | 7lg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/7lg3 ftp://data.pdbj.org/pub/pdb/validation_reports/lg/7lg3 | HTTPS FTP |
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-Related structure data
Related structure data | 3h7bS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31725.088 Da / Num. of mol.: 1 / Fragment: UNP residues 25-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: U5YJM1, UniProt: A0A140T913*PLUS | ||||
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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.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769 | ||||
#3: Protein/peptide | Mass: 1089.329 Da / Num. of mol.: 1 / Fragment: UNP residues 3896-3894 / Source method: obtained synthetically Source: (synth.) Severe acute respiratory syndrome coronavirus 2 References: UniProt: P0DTD1 | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.3 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 20% PEG4000, 0.1 M sodium acetate, pH 5.6, 20% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 9, 2020 / Details: SI 111 CRYSTAL |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→49.67 Å / Num. obs: 20879 / % possible obs: 99.3 % / Redundancy: 4.7 % / CC1/2: 0.982 / CC star: 0.995 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.093 / Rrim(I) all: 0.218 / Χ2: 1.015 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1005 / CC1/2: 0.37 / CC star: 0.73 / Χ2: 0.87 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3H7B Resolution: 2.3→45.74 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.917 / SU B: 19.002 / SU ML: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.318 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.54 Å2 / Biso mean: 37.644 Å2 / Biso min: 22.76 Å2
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Refinement step | Cycle: final / Resolution: 2.3→45.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.301→2.361 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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