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Open data
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Basic information
Entry | Database: PDB / ID: 1g0x | ||||||
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Title | CRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN OF LIR-1 (ILT2) | ||||||
![]() | LEUCOCYTE IMMUNOGLOBULIN-LIKE RECEPTOR-1 | ||||||
![]() | IMMUNE SYSTEM / Immunoglobulin fold / 3-10 helix | ||||||
Function / homology | ![]() HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / MHC class Ib protein complex binding / HLA-B specific inhibitory MHC class I receptor activity / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / Fc receptor mediated inhibitory signaling pathway / MHC class Ib protein binding / MHC class Ib receptor activity ...HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / MHC class Ib protein complex binding / HLA-B specific inhibitory MHC class I receptor activity / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / Fc receptor mediated inhibitory signaling pathway / MHC class Ib protein binding / MHC class Ib receptor activity / negative regulation of T cell mediated cytotoxicity / MHC class I receptor activity / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of transforming growth factor beta production / negative regulation of alpha-beta T cell activation / negative regulation of cytokine production involved in immune response / negative regulation of serotonin secretion / negative regulation of natural killer cell mediated cytotoxicity / dendritic cell differentiation / negative regulation of mononuclear cell proliferation / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / protein phosphatase 1 binding / negative regulation of osteoclast development / negative regulation of interleukin-12 production / negative regulation of endocytosis / negative regulation of interferon-beta production / negative regulation of dendritic cell apoptotic process / positive regulation of macrophage cytokine production / negative regulation of interleukin-10 production / MHC class I protein binding / negative regulation of calcium ion transport / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / negative regulation of cell cycle / T cell proliferation involved in immune response / negative regulation of T cell proliferation / positive regulation of defense response to virus by host / SH2 domain binding / response to virus / receptor internalization / cytokine-mediated signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / cellular response to lipopolysaccharide / defense response to virus / adaptive immune response / positive regulation of apoptotic process / external side of plasma membrane / positive regulation of gene expression / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chapman, T.L. / Heikema, A.P. / West Jr., A.P. / Bjorkman, P.J. | ||||||
![]() | ![]() Title: Crystal structure and ligand binding properties of the D1D2 region of the inhibitory receptor LIR-1 (ILT2). Authors: Chapman, T.L. / Heikema, A.P. / West Jr., A.P. / Bjorkman, P.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.5 KB | Display | ![]() |
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PDB format | ![]() | 40.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 362.3 KB | Display | ![]() |
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Full document | ![]() | 365.6 KB | Display | |
Data in XML | ![]() | 5.4 KB | Display | |
Data in CIF | ![]() | 8.9 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: 21998.645 Da / Num. of mol.: 1 / Fragment: D1D2 LIGAND BINDING 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: 3.43 Å3/Da / Density % sol: 64.16 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: potassium sodium tartarate, tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ | ||||||||||||||||||||||||
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: Dec 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 21555 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.297 / Num. unique all: 2112 / % possible all: 99.5 |
Reflection | *PLUS Lowest resolution: 30 Å / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 99.5 % / Num. unique obs: 2112 / Mean I/σ(I) obs: 3.6 |
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Processing
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Refinement | Resolution: 2.1→19.77 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1902676.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.83 Å2 / ksol: 0.361 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.17 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
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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: 4.9 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 29.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.287 / % reflection Rfree: 5.5 % / Rfactor Rwork: 0.226 |