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- PDB-1p1z: X-RAY CRYSTAL STRUCTURE OF THE LECTIN-LIKE NATURAL KILLER CELL RE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1p1z | ||||||
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Title | X-RAY CRYSTAL STRUCTURE OF THE LECTIN-LIKE NATURAL KILLER CELL RECEPTOR LY-49C BOUND TO ITS MHC CLASS I LIGAND H-2Kb | ||||||
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![]() | IMMUNE SYSTEM / NK / Kb / MHC / Antigenic Peptide / Ly49 / OVA | ||||||
Function / homology | ![]() intracellular amino acid homeostasis / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / phagolysosome / monoatomic ion homeostasis / response to steroid hormone / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / embryo development ending in birth or egg hatching / ER-Phagosome pathway ...intracellular amino acid homeostasis / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / phagolysosome / monoatomic ion homeostasis / response to steroid hormone / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / embryo development ending in birth or egg hatching / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / response to corticosterone / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / monoatomic ion transport / phagocytic vesicle / Neutrophil degranulation / early endosome lumen / Neutrophil degranulation / response to progesterone / 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 / peptide binding / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / response to estrogen / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / carbohydrate binding / protein homotetramerization / intracellular iron ion homeostasis / protease binding / vesicle / amyloid fibril formation / learning or memory / cell adhesion / defense response to bacterium / immune response / lysosomal membrane / external side of plasma membrane / intracellular membrane-bounded organelle / signaling receptor binding / calcium ion binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular region / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dimasi, N. / Natarajan, K. / Rangjin, G. / Dam, J. / Margulies, D.H. / Mariuzza, R.A. | ||||||
![]() | ![]() Title: Variable MHC class I engagement by Ly49 natural killer cell receptors demonstrated by the crystal structure of Ly49C bound to H-2K(b). Authors: Dam, J. / Guan, R. / Natarajan, K. / Dimasi, N. / Chlewicki, L.K. / Kranz, D.M. / Schuck, P. / Margulies, D.H. / Mariuzza, R.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 | ![]() | 107.8 KB | Display | ![]() |
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PDB format | ![]() | 88.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.1 KB | Display | ![]() |
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Full document | ![]() | 514 KB | Display | |
Data in XML | ![]() | 26.5 KB | Display | |
Data in CIF | ![]() | 35.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 31648.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 11704.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 964.137 Da / Num. of mol.: 1 / Fragment: residues 257-264 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Gallus gallus (chicken). References: UniProt: P01012 |
#4: Protein | Mass: 14369.787 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.61 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 10% PEG 20000, 2% DIOXANE, 0.1 M Bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
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: Nov 10, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.26→50 Å / Num. all: 32168 / Num. obs: 32168 / % possible obs: 99.5 % / Observed criterion σ(F): 2.8 / Observed criterion σ(I): 3.2 / Rmerge(I) obs: 0.096 |
Reflection shell | Resolution: 3.26→3.28 Å / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5.3 / Rsym value: 0.31 / % possible all: 99.6 |
Reflection | *PLUS Num. obs: 12168 |
Reflection shell | *PLUS Lowest resolution: 3.31 Å / % possible obs: 99.8 % / Num. unique obs: 596 / Rmerge(I) obs: 0.264 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 3.26→50 Å
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Refinement | *PLUS Num. reflection obs: 11771 / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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