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Yorodumi- PDB-6aed: Crystal Structure of the four Ig-like domain of LILRB2(LIR2/ILT4/... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6aed | ||||||
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Title | Crystal Structure of the four Ig-like domain of LILRB2(LIR2/ILT4/CD85d) | ||||||
Components | Leukocyte immunoglobulin-like receptor subfamily B member 2 | ||||||
Keywords | IMMUNE SYSTEM / leukocyte immunoglobulin-like receptor | ||||||
Function / homology | Function and homology information negative regulation of antigen processing and presentation / negative regulation of postsynaptic density organization / interleukin-10-mediated signaling pathway / negative regulation of T cell costimulation / positive regulation of tolerance induction / MHC class Ib protein complex binding / inhibitory MHC class I receptor activity / immune response-inhibiting cell surface receptor signaling pathway / MHC class Ib protein binding / Fc receptor mediated inhibitory signaling pathway ...negative regulation of antigen processing and presentation / negative regulation of postsynaptic density organization / interleukin-10-mediated signaling pathway / negative regulation of T cell costimulation / positive regulation of tolerance induction / MHC class Ib protein complex binding / inhibitory MHC class I receptor activity / immune response-inhibiting cell surface receptor signaling pathway / MHC class Ib protein binding / Fc receptor mediated inhibitory signaling pathway / positive regulation of long-term synaptic depression / positive regulation of T cell tolerance induction / protein phosphatase 1 binding / positive regulation of regulatory T cell differentiation / regulation of dendritic cell differentiation / negative regulation of protein metabolic process / regulation of long-term synaptic potentiation / heterotypic cell-cell adhesion / tertiary granule membrane / negative regulation of calcium ion transport / ficolin-1-rich granule membrane / MHC class I protein binding / cellular defense response / positive regulation of protein dephosphorylation / negative regulation of T cell proliferation / positive regulation of T cell proliferation / cell adhesion molecule binding / positive regulation of interleukin-6 production / cytokine-mediated signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell signaling / amyloid-beta binding / cellular response to lipopolysaccharide / adaptive immune response / learning or memory / cell surface receptor signaling pathway / immune response / Neutrophil degranulation / protein-containing complex binding / cell surface / signal transduction / protein homodimerization activity / extracellular space / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.797 Å | ||||||
Authors | Wang, Q. / Song, H. / Qi, J. / Gao, G.F. | ||||||
Citation | Journal: Cell. Mol. Immunol. / Year: 2019 Title: Structures of the four Ig-like domain LILRB2 and the four-domain LILRB1 and HLA-G1 complex. Authors: Wang, Q. / Song, H. / Cheng, H. / Qi, J. / Nam, G. / Tan, S. / Wang, J. / Fang, M. / Shi, Y. / Tian, Z. / Cao, X. / An, Z. / Yan, J. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6aed.cif.gz | 162.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aed.ent.gz | 128.6 KB | Display | PDB format |
PDBx/mmJSON format | 6aed.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/6aed ftp://data.pdbj.org/pub/pdb/validation_reports/ae/6aed | HTTPS FTP |
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-Related structure data
Related structure data | 6aeeC 2gw5S 4llaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43579.008 Da / Num. of mol.: 1 / Fragment: UNP residues 27-419 / Mutation: V213M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LILRB2 / Production host: Trichoplusia ni (cabbage looper) / Variant (production host): Hi5 / References: UniProt: Q8N423 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.44 Å3/Da / Density % sol: 80.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris, pH 8.5, 25%(v/v) tert-butanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.797→50 Å / Num. obs: 11011 / % possible obs: 99.9 % / Redundancy: 9.8 % / Net I/σ(I): 16.83 |
Reflection shell | Resolution: 3.8→3.94 Å / Num. unique obs: 1114 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GW5, 4LLA Resolution: 3.797→42.752 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.78
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.797→42.752 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 4.076 Å / Origin y: -65.0019 Å / Origin z: 5.175 Å
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Refinement TLS group | Selection details: all |