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- PDB-2dyp: Crystal Structure of LILRB2(LIR2/ILT4/CD85d) complexed with HLA-G -

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Basic information

Entry
Database: PDB / ID: 2dyp
TitleCrystal Structure of LILRB2(LIR2/ILT4/CD85d) complexed with HLA-G
Components
  • 9 Mer Peptide From Histone H2A.x
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, alpha chain G
  • Leukocyte immunoglobulin-like receptor subfamily B member 2
KeywordsIMMUNE SYSTEM / Immunoglobulin-like
Function / homology
Function and homology information


negative regulation of antigen processing and presentation / negative regulation of postsynaptic density organization / 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 / immune response-inhibiting cell surface receptor signaling pathway / negative regulation of dendritic cell differentiation / Fc receptor mediated inhibitory signaling pathway ...negative regulation of antigen processing and presentation / negative regulation of postsynaptic density organization / 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 / immune response-inhibiting cell surface receptor signaling pathway / negative regulation of dendritic cell differentiation / Fc receptor mediated inhibitory signaling pathway / MHC class Ib protein binding / positive regulation of natural killer cell cytokine production / positive regulation of long-term synaptic depression / negative regulation of T cell mediated cytotoxicity / immune response-regulating signaling pathway / cis-Golgi network membrane / interleukin-10-mediated signaling pathway / negative regulation of immune response / positive regulation of T cell tolerance induction / protein phosphatase 1 binding / negative regulation of G0 to G1 transition / chromatin-protein adaptor activity / XY body / regulation of dendritic cell differentiation / protein localization to site of double-strand break / negative regulation of natural killer cell mediated cytotoxicity / filopodium membrane / regulation of long-term synaptic potentiation / heterotypic cell-cell adhesion / positive regulation of regulatory T cell differentiation / negative regulation of protein metabolic process / positive regulation of macrophage cytokine production / CD8 receptor binding / response to ionizing radiation / protein homotrimerization / MHC class I protein binding / negative regulation of calcium ion transport / site of DNA damage / tertiary granule membrane / protection from natural killer cell mediated cytotoxicity / ficolin-1-rich granule membrane / positive regulation of endothelial cell apoptotic process / 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 / cellular defense response / Replacement of protamines by nucleosomes in the male pronucleus / positive regulation of T cell proliferation / Packaging Of Telomere Ends / cell adhesion molecule binding / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / negative regulation of T cell proliferation / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / positive regulation of interleukin-12 production / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / male germ cell nucleus / DNA methylation / positive regulation of DNA repair / : / : / Condensation of Prophase Chromosomes / negative regulation of angiogenesis / positive regulation of receptor binding / Chromatin modifications during the maternal to zygotic transition (MZT) / DNA damage checkpoint signaling / early endosome lumen / SIRT1 negatively regulates rRNA expression / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / condensed nuclear chromosome / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / replication fork / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / meiotic cell cycle / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / peptide antigen assembly with MHC class II protein complex / Transcriptional regulation by small RNAs / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / Formation of the beta-catenin:TCF transactivating complex / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Histone H2A conserved site / Histone H2A signature. / Class I Histocompatibility antigen, domains alpha 1 and 2 ...: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Histone H2A conserved site / Histone H2A signature. / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Histone H2AX / HLA class I histocompatibility antigen, alpha chain G / Beta-2-microglobulin / Leukocyte immunoglobulin-like receptor subfamily B member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShiroishi, M. / Kuroki, K. / Rasubala, L. / Kohda, D. / Maenaka, K.
CitationJournal: 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
DepositionSep 15, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, alpha chain G
B: Beta-2-microglobulin
C: 9 Mer Peptide From Histone H2A.x
D: Leukocyte immunoglobulin-like receptor subfamily B member 2


Theoretical massNumber of molelcules
Total (without water)66,9424
Polymers66,9424
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.400, 81.400, 186.733
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe interaction between HLA-G (the molecule composed of chain A/B/C) and LILRB2 (chain D) is a biological unit.

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Components

#1: Protein HLA class I histocompatibility antigen, alpha chain G / HLA G antigen


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
#2: Protein Beta-2-microglobulin


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 9 Mer Peptide From Histone H2A.x


Mass: 1148.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This peptide was chemically synthesized / References: UniProt: P16104
#4: Protein Leukocyte immunoglobulin-like receptor subfamily B member 2 / Leukocyte immunoglobulin-like receptor 2 / LIR-2 / Immunoglobulin- like transcript 4 / ILT-4 / ...Leukocyte immunoglobulin-like receptor 2 / LIR-2 / Immunoglobulin- like transcript 4 / ILT-4 / Monocyte/macrophage immunoglobulin-like receptor 10 / MIR-10 / CD85d antigen


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 / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl pH8.0, 45% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.5→2.59 Å / Redundancy: 11 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 3.5 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2D31, 2GW5

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
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1825 7.2 %Random
Rwork0.233 ---
obs-25424 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.1963 Å2 / ksol: 0.342353 e/Å3
Displacement parametersBiso mean: 60.2 Å2
Baniso -1Baniso -2Baniso -3
1-7.72 Å29.54 Å20 Å2
2--7.72 Å20 Å2
3----15.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4610 0 0 86 4696
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d1
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 303 7.3 %
Rwork0.287 3844 -
obs-645 99.5 %

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