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Yorodumi- PDB-8gqv: The Crystal Structures of a Swine SLA-2*HB01 Molecules Complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gqv | ||||||
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Title | The Crystal Structures of a Swine SLA-2*HB01 Molecules Complexed with a CTL epitope from Asia1 serotype of Foot-and-mouth disease virus | ||||||
Components |
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Keywords | IMMUNE SYSTEM/EPITOPE / SLA-2 / foot-and-mouth disease virus / crystal / peptide / epitope / CTL / Complex / Peptide presentation / universal vaccine candidate / IMMUNE SYSTEM / IMMUNE SYSTEM-EPITOPE complex | ||||||
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 / antigen processing and presentation / 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 / antigen processing and presentation / 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) Foot-and-mouth disease virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Feng, L. / Gao, Y.Y. / Sun, M.W. / Li, Z.B. / Zhang, Q. / Yang, J. / Qiao, C. / Jin, H. / Feng, H.S. / Xian, Y.H. ...Feng, L. / Gao, Y.Y. / Sun, M.W. / Li, Z.B. / Zhang, Q. / Yang, J. / Qiao, C. / Jin, H. / Feng, H.S. / Xian, Y.H. / Qi, J.X. / Gao, G.F. / Liu, W.J. / Gao, F.S. | ||||||
Funding support | China, 1items
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Citation | Journal: Cells / Year: 2022 Title: The Parallel Presentation of Two Functional CTL Epitopes Derived from the O and Asia 1 Serotypes of Foot-and-Mouth Disease Virus and Swine SLA-2*HB01: Implications for Universal Vaccine Development. Authors: Feng, L. / Gao, Y.Y. / Sun, M. / Li, Z.B. / Zhang, Q. / Yang, J. / Qiao, C. / Jin, H. / Feng, H.S. / Xian, Y.H. / Qi, J. / Gao, G.F. / Liu, W.J. / Gao, F.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gqv.cif.gz | 322.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gqv.ent.gz | 262.9 KB | Display | PDB format |
PDBx/mmJSON format | 8gqv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gqv_validation.pdf.gz | 462.2 KB | Display | wwPDB validaton report |
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Full document | 8gqv_full_validation.pdf.gz | 474.1 KB | Display | |
Data in XML | 8gqv_validation.xml.gz | 30.3 KB | Display | |
Data in CIF | 8gqv_validation.cif.gz | 42.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/8gqv ftp://data.pdbj.org/pub/pdb/validation_reports/gq/8gqv | HTTPS FTP |
-Related structure data
Related structure data | 8gqwC 1q94S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31746.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: SLA-2 / Production host: Escherichia coli (E. coli) / References: UniProt: E3WHS2 #2: Protein | Mass: 11431.918 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Production host: Escherichia coli (E. coli) / References: UniProt: Q07717 #3: Protein/peptide | Mass: 1058.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Foot-and-mouth disease virus #4: Water | ChemComp-HOH / | |
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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: 2.23 Å3/Da / Density % sol: 44.87 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: Ammonium acetate, PEG, BIS-TRIS |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: MAATEL IMAGINE / Detector: IMAGE PLATE / Date: Oct 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 31827 / % possible obs: 99.2 % / Redundancy: 7 % / Biso Wilson estimate: 33.63 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.318 / Num. unique obs: 31827 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Q94 Resolution: 2.4→48.202 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.7 / 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: 158.75 Å2 / Biso mean: 46.2 Å2 / Biso min: 15.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→48.202 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -12.7487 Å / Origin y: -41.0208 Å / Origin z: 14.1495 Å
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Refinement TLS group |
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