[English] 日本語
![](img/lk-miru.gif)
- PDB-2dyp: Crystal Structure of LILRB2(LIR2/ILT4/CD85d) complexed with HLA-G -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2dyp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of LILRB2(LIR2/ILT4/CD85d) complexed with HLA-G | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM / Immunoglobulin-like | ||||||
Function / homology | ![]() 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 / Fc receptor mediated inhibitory signaling pathway / MHC class Ib protein binding / positive regulation of long-term synaptic depression / positive regulation of natural killer cell cytokine production / negative regulation of T cell mediated cytotoxicity / cis-Golgi network membrane / positive regulation of T cell tolerance induction / negative regulation of natural killer cell mediated cytotoxicity / protein phosphatase 1 binding / negative regulation of G0 to G1 transition / negative regulation of immune response / positive regulation of endothelial cell apoptotic process / XY body / positive regulation of regulatory T cell differentiation / regulation of dendritic cell differentiation / filopodium membrane / regulation of long-term synaptic potentiation / heterotypic cell-cell adhesion / positive regulation of macrophage cytokine production / negative regulation of protein metabolic process / response to ionizing radiation / CD8 receptor binding / MHC class I protein binding / protein homotrimerization / site of DNA damage / tertiary granule membrane / negative regulation of calcium ion transport / ficolin-1-rich granule membrane / protection from natural killer cell mediated cytotoxicity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular defense response / Replacement of protamines by nucleosomes in the male pronucleus / heterochromatin organization / Packaging Of Telomere Ends / negative regulation of T cell proliferation / positive regulation of T cell proliferation / 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 / nucleosomal DNA binding / cell adhesion molecule binding / 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 DNA repair / positive regulation of interleukin-12 production / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / 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) / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / meiotic cell cycle / PRC2 methylates histones and DNA / positive regulation of receptor binding / condensed nuclear chromosome / early endosome lumen / replication fork / DNA damage checkpoint signaling / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / male germ cell nucleus / Defective pyroptosis / 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 / cellular response to iron ion / RNA Polymerase I Promoter Escape / Endosomal/Vacuolar pathway / Nonhomologous End-Joining (NHEJ) / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / double-strand break repair via homologous recombination / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / negative regulation of forebrain neuron differentiation / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shiroishi, M. / Kuroki, K. / Rasubala, L. / Kohda, D. / Maenaka, K. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 129 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 99.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 467.5 KB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 32.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
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.) ![]() ![]() ![]() |
---|---|
#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.) ![]() ![]() ![]() |
#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.) ![]() ![]() ![]() |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.84 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| ||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.1963 Å2 / ksol: 0.342353 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 60.2 Å2
| ||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→46.66 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
|