[English] 日本語
Yorodumi
- PDB-2dyp: Crystal Structure of LILRB2(LIR2/ILT4/CD85d) complexed with HLA-G -

+
Open data


ID or keywords:

Loading...

-
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 T cell costimulation / peripheral B cell tolerance induction / positive regulation of tolerance induction / MHC class Ib protein complex binding / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / Fc receptor mediated inhibitory signaling pathway / negative regulation of postsynaptic density organization ...negative regulation of antigen processing and presentation / negative regulation of T cell costimulation / peripheral B cell tolerance induction / positive regulation of tolerance induction / MHC class Ib protein complex binding / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / Fc receptor mediated inhibitory signaling pathway / negative regulation of postsynaptic density organization / positive regulation of natural killer cell cytokine production / positive regulation of long-term synaptic depression / MHC class Ib protein binding / negative regulation of T cell mediated cytotoxicity / immune response-regulating signaling pathway / cis-Golgi network membrane / negative regulation of immune response / positive regulation of T cell tolerance induction / interleukin-10-mediated signaling pathway / protein phosphatase 1 binding / negative regulation of G0 to G1 transition / regulation of dendritic cell differentiation / XY body / chromatin-protein adaptor activity / protein localization to site of double-strand break / negative regulation of natural killer cell mediated cytotoxicity / regulation of long-term synaptic potentiation / filopodium membrane / negative regulation of protein metabolic process / heterotypic cell-cell adhesion / positive regulation of regulatory T cell differentiation / positive regulation of macrophage cytokine production / response to ionizing radiation / CD8 receptor binding / protein homotrimerization / negative regulation of calcium ion transport / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / tertiary granule membrane / site of DNA damage / ficolin-1-rich granule membrane / positive regulation of endothelial cell apoptotic process / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular defense response / Replacement of protamines by nucleosomes in the male pronucleus / cell adhesion molecule binding / negative regulation of T cell proliferation / Packaging Of Telomere Ends / positive regulation of T cell proliferation / positive regulation of interleukin-12 production / 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 / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / positive regulation of DNA repair / negative regulation of receptor binding / DNA damage checkpoint signaling / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / negative regulation of angiogenesis / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / DNA methylation / Condensation of Prophase Chromosomes / replication fork / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / transferrin transport / condensed nuclear chromosome / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / cellular response to iron ion / PRC2 methylates histones and DNA / Endosomal/Vacuolar pathway / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / meiotic cell cycle / male germ cell nucleus / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / Transcriptional regulation by small RNAs / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor 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 / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type ...: / 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 / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / 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 domain / Histone-fold / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more