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Yorodumi- PDB-2dyp: Crystal Structure of LILRB2(LIR2/ILT4/CD85d) complexed with HLA-G -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dyp | ||||||
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Title | Crystal Structure of LILRB2(LIR2/ILT4/CD85d) complexed with HLA-G | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Immunoglobulin-like | ||||||
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 / peripheral B cell tolerance induction / positive regulation of tolerance induction / MHC class Ib protein complex binding / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor 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 / peripheral B cell tolerance induction / positive regulation of tolerance induction / MHC class Ib protein complex binding / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / 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 / negative regulation of T cell mediated cytotoxicity / positive regulation of T cell tolerance induction / protein phosphatase 1 binding / XY body / negative regulation of G0 to G1 transition / negative regulation of immune response / positive regulation of regulatory T cell differentiation / positive regulation of endothelial cell apoptotic process / regulation of dendritic cell differentiation / filopodium membrane / negative regulation of protein metabolic process / positive regulation of natural killer cell cytokine production / regulation of long-term synaptic potentiation / heterotypic cell-cell adhesion / cis-Golgi network membrane / positive regulation of macrophage cytokine production / negative regulation of natural killer cell mediated cytotoxicity / response to ionizing radiation / protein homotrimerization / site of DNA damage / tertiary granule membrane / negative regulation of calcium ion transport / ficolin-1-rich granule membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / CD8 receptor binding / MHC class I protein binding / cellular defense response / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / positive regulation of protein dephosphorylation / Deposition of new CENPA-containing nucleosomes at the centromere / negative regulation of T cell proliferation / protection from natural killer cell mediated cytotoxicity / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / positive regulation of T cell proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / positive regulation of DNA repair / Inhibition of DNA recombination at telomere / Meiotic synapsis / positive regulation of interleukin-12 production / RNA Polymerase I Promoter Opening / cell adhesion molecule binding / Assembly of the ORC complex at the origin of replication / negative regulation of angiogenesis / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / replication fork / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / meiotic cell cycle / PRC2 methylates histones and DNA / early endosome lumen / positive regulation of receptor binding / DNA damage checkpoint signaling / condensed nuclear chromosome / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / male germ cell nucleus / negative regulation of receptor binding / Defective pyroptosis / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Transcriptional regulation by small RNAs / double-strand break repair via homologous recombination / Formation of the beta-catenin:TCF transactivating complex / cellular response to gamma radiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / negative regulation of forebrain neuron differentiation / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / ER to Golgi transport vesicle membrane / B-WICH complex positively regulates rRNA expression / response to molecule of bacterial origin / regulation of erythrocyte differentiation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Shiroishi, M. / Kuroki, K. / Rasubala, L. / Kohda, D. / Maenaka, K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Structural basis for recognition of the nonclassical MHC molecule HLA-G by the leukocyte Ig-like receptor B2 (LILRB2/LIR2/ILT4/CD85d) Authors: Shiroishi, M. / Kuroki, K. / Rasubala, L. / Tsumoto, K. / Kumagai, I. / Kurimoto, E. / Kato, K. / Kohda, D. / Maenaka, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dyp.cif.gz | 129 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dyp.ent.gz | 99.9 KB | Display | PDB format |
PDBx/mmJSON format | 2dyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/2dyp ftp://data.pdbj.org/pub/pdb/validation_reports/dy/2dyp | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The interaction between HLA-G (the molecule composed of chain A/B/C) and LILRB2 (chain D) is a biological unit. |
-Components
#1: Protein | Mass: 32017.492 Da / Num. of mol.: 1 / Fragment: residues in data base 25-300 / Mutation: C42S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P17693 |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: residues in data base 24-219 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1148.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This peptide was chemically synthesized / References: UniProt: P16104 |
#4: Protein | Mass: 21896.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8N423 |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris-HCl pH8.0, 45% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 25468 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 10.8 % / Biso Wilson estimate: 56.3 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 11 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 3.5 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2D31, 2GW5 Resolution: 2.5→46.66 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1719921.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Maximum Likelihood
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.1963 Å2 / ksol: 0.342353 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 60.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→46.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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