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- PDB-1hyr: CRYSTAL STRUCTURE OF HUMAN MICA IN COMPLEX WITH NATURAL KILLER CE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1hyr | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN MICA IN COMPLEX WITH NATURAL KILLER CELL RECEPTOR NKG2D | ||||||
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![]() | IMMUNE SYSTEM / ACTIVATING NK CELL RECEPTOR / NKG2D / C-TYPE-LECTIN LIKE / MIC-A / MHC-I / COMPLEX | ||||||
Function / homology | ![]() immune response to tumor cell / negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / cytolysis / gamma-delta T cell activation / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell mediated cytotoxicity ...immune response to tumor cell / negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / cytolysis / gamma-delta T cell activation / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell mediated cytotoxicity / natural killer cell activation / negative regulation of GTPase activity / MHC class I protein binding / plasma membrane => GO:0005886 / stimulatory C-type lectin receptor signaling pathway / regulation of immune response / T cell costimulation / nitric oxide biosynthetic process / viral process / DAP12 interactions / 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 / T cell mediated cytotoxicity / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of nitric oxide biosynthetic process / positive regulation of type II interferon production / DAP12 signaling / signaling receptor activity / response to heat / carbohydrate binding / cellular response to lipopolysaccharide / defense response to virus / adaptive immune response / killing of cells of another organism / cell differentiation / defense response to Gram-positive bacterium / defense response to bacterium / immune response / external side of plasma membrane / signaling receptor binding / DNA damage response / cell surface / signal transduction / extracellular space / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, P. / Strong, R.K. | ||||||
![]() | ![]() Title: Complex structure of the activating immunoreceptor NKG2D and its MHC class I-like ligand MICA. Authors: Li, P. / Morris, D.L. / Willcox, B.E. / Steinle, A. / Spies, T. / Strong, R.K. #1: ![]() Title: Crystal Structure of the MHC Class I Homolog Mic-A, a Gammadelta T Cell Ligand Authors: Li, P. / Willie, S.T. / Bauer, S. / Morris, D.L. / Spies, T. / Strong, R.K. #2: ![]() Title: ACTIVATION OF NK CELLS AND T CELLS BY NKG2D, A RECEPTOR FOR STRESS INDUCIBLE MICA Authors: Bauer, S. / Groh, V. / Wu, J. / Steinle, A. / Phillips, J.H. / Lanier, L.L. / Spies, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.8 KB | Display | ![]() |
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PDB format | ![]() | 86.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 380.1 KB | Display | ![]() |
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Full document | ![]() | 400.7 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 20.4 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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Unit cell |
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Components
#1: Protein | Mass: 15849.903 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN (RESIDUES 80 TO 216) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 31731.434 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN (RESIDUES 1 TO 274) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 58.3 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: (NH4)2SO4, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2000 | ||||||||||||||||||
Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.7→30 Å / Num. all: 256599 / Num. obs: 21938 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 66.1 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 34 | ||||||||||||||||||
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 9 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2150 / Rsym value: 0.425 / % possible all: 100 | ||||||||||||||||||
Reflection | *PLUS Num. measured all: 256599 / Rmerge(I) obs: 0.076 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 100 % |
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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: 33.93 Å2 / ksol: 0.302 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→29.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.025 / 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: 7.4 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 59.8 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.397 / % reflection Rfree: 7.5 % / Rfactor Rwork: 0.346 |