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- PDB-6kwn: Crystal structure of pSLA-1*1301(F99Y) complex with S-OIV-derived... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6kwn | ||||||
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Title | Crystal structure of pSLA-1*1301(F99Y) complex with S-OIV-derived epitope NSDTVGWSW | ||||||
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![]() | STRUCTURAL PROTEIN / MHC class I structure / A single-amino acid mutation / Peptide motifs / Random peptide library | ||||||
Function / homology | ![]() 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 / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity ...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 / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / antigen processing and presentation / viral budding from plasma 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 / carbohydrate metabolic process / immune response / lysosomal membrane / host cell plasma membrane / virion membrane / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wei, X.H. / Wang, S. / Zhang, N.Z. / Xia, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Peptidomes and Structures Illustrate Two Distinguishing Mechanisms of Alternating the Peptide Plasticity Caused by Swine MHC Class I Micropolymorphism. Authors: Wei, X. / Wang, S. / Li, Z. / Li, Z. / Qu, Z. / Wang, S. / Zou, B. / Liang, R. / Xia, C. / Zhang, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.7 KB | Display | ![]() |
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PDB format | ![]() | 68.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.1 KB | Display | ![]() |
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Full document | ![]() | 451.5 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kwkC ![]() 6kwlC ![]() 6kwoC ![]() 3qq3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31622.965 Da / Num. of mol.: 1 / Mutation: F99Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 11579.093 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1051.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M Bis-Tris pH 6.5, 20% w/v Polyethylene Glycol Monomethyl ether 5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→50 Å / Num. obs: 17844 / % possible obs: 98.3 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.159 / Rsym value: 0.159 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.37→2.41 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 5.7 / Num. unique obs: 17844 / Rsym value: 0.241 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3qq3 Resolution: 2.4→41.824 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.859 / SU B: 0.005 / SU ML: 0 / Cross valid method: NONE / ESU R: 0.291 / ESU R Free: 0.337 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.866 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→41.824 Å
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LS refinement shell |
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