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- PDB-1hq8: CRYSTAL STRUCTURE OF THE MURINE NK CELL-ACTIVATING RECEPTOR NKG2D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1hq8 | ||||||
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Title | CRYSTAL STRUCTURE OF THE MURINE NK CELL-ACTIVATING RECEPTOR NKG2D AT 1.95 A | ||||||
![]() | NKG2-D | ||||||
![]() | APOPTOSIS / homodimer / cis-proline | ||||||
Function / homology | ![]() positive regulation of myeloid dendritic cell activation / negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell mediated cytotoxicity / natural killer cell activation / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / MHC class I protein binding ...positive regulation of myeloid dendritic cell activation / negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell mediated cytotoxicity / natural killer cell activation / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / MHC class I protein binding / stimulatory C-type lectin receptor signaling pathway / nitric oxide biosynthetic process / kinase binding / positive regulation of nitric oxide biosynthetic process / positive regulation of type II interferon production / signaling receptor activity / carbohydrate binding / cellular response to lipopolysaccharide / adaptive immune response / cell differentiation / defense response to Gram-positive bacterium / positive regulation of apoptotic process / external side of plasma membrane / cell surface / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wolan, D.W. / Teyton, L. / Rudolph, M.G. / Villmow, B. / Bauer, S. / Busch, D.H. / Wilson, I.A. | ||||||
![]() | ![]() Title: Crystal structure of the murine NK cell-activating receptor NKG2D at 1.95 A. Authors: Wolan, D.W. / Teyton, L. / Rudolph, M.G. / Villmow, B. / Bauer, S. / Busch, D.H. / Wilson, I.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 34.3 KB | Display | ![]() |
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PDB format | ![]() | 26.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.9 KB | Display | ![]() |
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Full document | ![]() | 427.7 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 10.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Details | The second part of the biological assembly is generated by the two fold axis: -x, 1/2-y, z |
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Components
#1: Protein | Mass: 14114.836 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.65 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: NaCl, Na-Cit., PEG400, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. all: 13874 / % possible obs: 98.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1361 / % possible all: 97.7 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 13874 |
Reflection shell | *PLUS % possible obs: 97.7 % / Num. unique obs: 1361 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.44 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→27.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.2 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 31.2 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.326 / % reflection Rfree: 9.6 % / Rfactor Rwork: 0.293 / Rfactor obs: 0.293 |