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Yorodumi- PDB-7ema: Mooring Stone-Like Arg114 Pulls Diverse Bulged Peptides: First In... -
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-Basic information
Entry | Database: PDB / ID: 7ema | ||||||
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Title | Mooring Stone-Like Arg114 Pulls Diverse Bulged Peptides: First Insight into African Swine Fever Virus-Derived T Cell Epitopes Presented by Swine Major Histocompatibility Complex Class I | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC I | ||||||
Function / homology | Function and homology information ER-Phagosome pathway / Endosomal/Vacuolar pathway / DAP12 interactions / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / DAP12 interactions / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / immune response / lysosomal membrane / extracellular region Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) uncultured virus (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Yue, C. / Xiang, W. / Huang, X. / Sun, Y. / Xiao, J. / Liu, K. / Sun, Z. / Qiao, P. / Li, H. / Gan, J. ...Yue, C. / Xiang, W. / Huang, X. / Sun, Y. / Xiao, J. / Liu, K. / Sun, Z. / Qiao, P. / Li, H. / Gan, J. / Ba, L. / Chai, Y. / Qi, J. / Liu, P. / Qi, P. / Zhao, Y. / Li, Y. / Qiu, H.J. / Gao, G.F. / Gao, G. / Liu, W.J. | ||||||
Citation | Journal: J.Virol. / Year: 2022 Title: Mooring Stone-Like Arg 114 Pulls Diverse Bulged Peptides: First Insight into African Swine Fever Virus-Derived T Cell Epitopes Presented by Swine Major Histocompatibility Complex Class I. Authors: Yue, C. / Xiang, W. / Huang, X. / Sun, Y. / Xiao, J. / Liu, K. / Sun, Z. / Qiao, P. / Li, H. / Gan, J. / Ba, L. / Chai, Y. / Qi, J. / Liu, P. / Qi, P. / Zhao, Y. / Li, Y. / Qiu, H.J. / Gao, ...Authors: Yue, C. / Xiang, W. / Huang, X. / Sun, Y. / Xiao, J. / Liu, K. / Sun, Z. / Qiao, P. / Li, H. / Gan, J. / Ba, L. / Chai, Y. / Qi, J. / Liu, P. / Qi, P. / Zhao, Y. / Li, Y. / Qiu, H.J. / Gao, G.F. / Gao, G. / Liu, W.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ema.cif.gz | 119.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ema.ent.gz | 72.2 KB | Display | PDB format |
PDBx/mmJSON format | 7ema.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/7ema ftp://data.pdbj.org/pub/pdb/validation_reports/em/7ema | HTTPS FTP |
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-Related structure data
Related structure data | 7em9C 7embC 7emcC 7emdC 3qq3S 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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Unit cell |
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-Components
#1: Protein | Mass: 31825.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: sla-, SLA-1 / Production host: Escherichia coli (E. coli) / References: UniProt: O19075 |
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#2: Protein | Mass: 11708.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: Q07717 |
#3: Protein/peptide | Mass: 984.059 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) uncultured virus (environmental samples) |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.41 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES pH 7.5, 30% w/v Polyethylene glycol 1,000. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.03997 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Dec 24, 2019 |
Radiation | Monochromator: 1.03997 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03997 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 36183 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 16.17 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 5.35 |
Reflection shell | Resolution: 1.8→1.87 Å / Rmerge(I) obs: 0.529 / Num. unique obs: 36183 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QQ3 Resolution: 1.8→26.82 Å / SU ML: 0.2218 / Cross valid method: NONE / σ(F): 1.41 / Phase error: 21.7708 / Stereochemistry target values: GeoStd + Monomer Library
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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 mean: 20.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→26.82 Å
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Refine LS restraints |
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LS refinement shell |
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