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Yorodumi- PDB-6kwl: Crystal structure of pSLA-1*0401(R156A) complex with FMDV-derived... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kwl | ||||||
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Title | Crystal structure of pSLA-1*0401(R156A) complex with FMDV-derived epitope MTAHITVPY | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / MHC class I structure / A single-amino acid mutation / Peptide motifs / Random peptide library | ||||||
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 / L-peptidase / modulation by virus of host chromatin organization / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I ...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 / L-peptidase / modulation by virus of host chromatin organization / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / 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 / nucleoside-triphosphate phosphatase / regulation of translation / protein complex oligomerization / MHC class II protein complex binding / late endosome membrane / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / immune response / induction by virus of host autophagy / RNA-directed RNA polymerase / lysosomal membrane / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / extracellular region / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) Foot-and-mouth disease virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Wei, X.H. / Wang, S. / Zhang, N.Z. / Xia, C. | ||||||
Funding support | China, 1items
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Citation | Journal: Front Immunol / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kwl.cif.gz | 180.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kwl.ent.gz | 139.6 KB | Display | PDB format |
PDBx/mmJSON format | 6kwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/6kwl ftp://data.pdbj.org/pub/pdb/validation_reports/kw/6kwl | HTTPS FTP |
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-Related structure data
Related structure data | 6kwkC 6kwnC 6kwoC 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: 31595.875 Da / Num. of mol.: 1 / Mutation: R156A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F6N4U7 |
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#2: Protein | Mass: 11431.918 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: 1033.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Foot-and-mouth disease virus / References: UniProt: P03311*PLUS |
#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 Å3/Da / Density % sol: 38.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M Sodium chloride, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97931 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 29750 / % possible obs: 97.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 18.924 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4 % / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 11.338 / Num. unique obs: 29750 / Rsym value: 0.137 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3qq3 Resolution: 1.8→35.712 Å / Cross valid method: NONE
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Refinement step | Cycle: LAST / Resolution: 1.8→35.712 Å
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LS refinement shell | Resolution: 1.8→1.86 Å |