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- PDB-1kpr: The human non-classical major histocompatibility complex molecule... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kpr | ||||||
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Title | The human non-classical major histocompatibility complex molecule HLA-E | ||||||
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Function / homology | ![]() positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation ...positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell proliferation / positive regulation of immunoglobulin production / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of interleukin-4 production / MHC class I protein binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Holmes, M.A. / Strong, R.K. | ||||||
![]() | ![]() Title: HLA-E allelic variants: Correlating differential expression, peptide affinities, crystal structures and thermal stabilities Authors: Strong, R.K. / Holmes, M.A. / Li, P. / Braun-Jones, L. / Lee, N. / Geraghty, D.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150.8 KB | Display | ![]() |
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PDB format | ![]() | 121.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ktlC ![]() 1mheS 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31511.596 Da / Num. of mol.: 2 / Mutation: R107G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein | ![]() Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #3: Protein/peptide | Mass: 1000.278 Da / Num. of mol.: 2 / Source method: obtained synthetically #4: Chemical | ChemComp-SO4 / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.58 Å3/Da / Density % sol: 73.13 % | ||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: ammonium sulfate, PEG 400, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP at 295K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 11, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.8→20 Å / Num. all: 39992 / Num. obs: 38312 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 83.3 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3850 / % possible all: 97.3 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. measured all: 299482 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 97.3 % / Mean I/σ(I) obs: 3.1 |
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Processing
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Refinement | Method to determine structure![]() Starting model: pdb entry 1MHE Resolution: 2.8→20 Å / Isotropic thermal model: isotropic group B's / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 63.9 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.9 Å
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 20 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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