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Yorodumi- PDB-6aee: Crystal structure of the four Ig-like domains of LILRB1 complexed... -
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-Basic information
Entry | Database: PDB / ID: 6aee | ||||||
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Title | Crystal structure of the four Ig-like domains of LILRB1 complexed with HLA-G | ||||||
Components |
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Keywords | IMMUNE SYSTEM / leukocyte immunoglobulin-like receptor / immunotherapy | ||||||
Function / homology | Function and homology information peripheral B cell tolerance induction / positive regulation of tolerance induction / 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 ...peripheral B cell tolerance induction / positive regulation of tolerance induction / 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 / positive regulation of natural killer cell cytokine production / negative regulation of T cell mediated cytotoxicity / MHC class I receptor activity / negative regulation of CD8-positive, alpha-beta T cell activation / cis-Golgi network membrane / negative regulation of transforming growth factor beta production / negative regulation of alpha-beta T cell activation / positive regulation of T cell tolerance induction / 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 G0 to G1 transition / negative regulation of interleukin-12 production / negative regulation of endocytosis / negative regulation of interferon-beta production / negative regulation of immune response / negative regulation of dendritic cell apoptotic process / positive regulation of endothelial cell apoptotic process / positive regulation of regulatory T cell differentiation / filopodium membrane / positive regulation of macrophage cytokine production / negative regulation of interleukin-10 production / CD8 receptor binding / MHC class I protein binding / protein homotrimerization / 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 / protection from natural killer cell mediated cytotoxicity / T cell proliferation involved in immune response / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein localization to CENP-A containing chromatin / cellular defense response / CENP-A containing nucleosome / heterochromatin organization / Packaging Of Telomere Ends / negative regulation of T cell proliferation / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / positive regulation of defense response to virus by host / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / positive regulation of interleukin-12 production / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SH2 domain binding / negative regulation of angiogenesis / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / PRC2 methylates histones and DNA / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Defective pyroptosis / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / HDACs deacetylate histones / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / RNA Polymerase I Promoter Escape / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / response to virus / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / negative regulation of forebrain neuron differentiation / NoRC negatively regulates rRNA expression Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.303 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 | 6aee.cif.gz | 305.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aee.ent.gz | 247.3 KB | Display | PDB format |
PDBx/mmJSON format | 6aee.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6aee_validation.pdf.gz | 481.6 KB | Display | wwPDB validaton report |
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Full document | 6aee_full_validation.pdf.gz | 505.1 KB | Display | |
Data in XML | 6aee_validation.xml.gz | 49.7 KB | Display | |
Data in CIF | 6aee_validation.cif.gz | 68.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/6aee ftp://data.pdbj.org/pub/pdb/validation_reports/ae/6aee | HTTPS FTP |
-Related structure data
Related structure data | 6aedC 2dypS 4ll9S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32046.559 Da / Num. of mol.: 2 / Fragment: UNP residues 25-300 / Mutation: C42S, L110I, Q115R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-G / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21(DE3) / References: UniProt: P17693 #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21(DE3) / References: UniProt: P61769 #3: Protein/peptide | Mass: 1148.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04908*PLUS #4: Protein | Mass: 44143.148 Da / Num. of mol.: 2 / Fragment: UNP residues 25-417 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LILRB1 / Production host: Trichoplusia ni (cabbage looper) / Variant (production host): Hi5 / References: UniProt: A0A0G2JQ44, UniProt: Q8NHL6*PLUS |
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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: 2.9 Å3/Da / Density % sol: 57.56 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2M imidazole malate, 15%(w/v) PEG4000, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97922 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97922 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 29866 / % possible obs: 99.9 % / Redundancy: 4.2 % / CC1/2: 0.972 / Rpim(I) all: 0.105 / Net I/σ(I): 7.89 |
Reflection shell | Resolution: 3.3→3.42 Å / Num. unique obs: 2993 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DYP, 4LL9 Resolution: 3.303→45.42 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.303→45.42 Å
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Refine LS restraints |
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LS refinement shell |
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