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- PDB-6kwl: Crystal structure of pSLA-1*0401(R156A) complex with FMDV-derived... -
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Open data
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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 | ||||||
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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 / 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 / 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 / lumenal side of endoplasmic reticulum membrane / host cell cytoplasmic vesicle membrane / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / 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 / MHC class II protein complex binding / protein complex oligomerization / late endosome membrane / regulation of translation / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / induction by virus of host autophagy / immune response / RNA-directed RNA polymerase / lysosomal membrane / external side of plasma membrane / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / signaling receptor binding / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / extracellular space / extracellular region / ATP binding / membrane 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 | ![]() | 180.6 KB | Display | ![]() |
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PDB format | ![]() | 139.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.3 KB | Display | ![]() |
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Full document | ![]() | 453.6 KB | Display | |
Data in XML | ![]() | 22.6 KB | Display | |
Data in CIF | ![]() | 34.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kwkC ![]() 6kwnC ![]() 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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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.) ![]() ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1033.220 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 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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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 |