[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-microglobulinBeta-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 / 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
Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A ...Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / MHC class I alpha chain, alpha1 alpha2 domains / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / MHC classes I/II-like antigen recognition protein / 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 / Immunoglobulins / Immunoglobulin-like fold / 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

-
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 / 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 / Water


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

-
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