2DYP

Crystal Structure of LILRB2(LIR2/ILT4/CD85d) complexed with HLA-G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for recognition of the nonclassical MHC molecule HLA-G by the leukocyte Ig-like receptor B2 (LILRB2/LIR2/ILT4/CD85d)

Shiroishi, M.Kuroki, K.Rasubala, L.Tsumoto, K.Kumagai, I.Kurimoto, E.Kato, K.Kohda, D.Maenaka, K.

(2006) Proc.Natl.Acad.Sci.Usa 103: 16412-16417

  • DOI: 10.1073/pnas.0605228103

  • PubMed Abstract: 
  • HLA-G is a nonclassical MHC class I (MHCI) molecule that can suppress a wide range of immune responses in the maternal-fetal interface. The human inhibitory immune receptors leukocyte Ig-like receptor (LILR) B1 [also called LIR1, Ig-like transcript 2 ...

    HLA-G is a nonclassical MHC class I (MHCI) molecule that can suppress a wide range of immune responses in the maternal-fetal interface. The human inhibitory immune receptors leukocyte Ig-like receptor (LILR) B1 [also called LIR1, Ig-like transcript 2 (ILT2), or CD85j] and LILRB2 (LIR2/ILT4/CD85d) preferentially recognize HLA-G. HLA-G inherently exhibits various forms, including beta(2)-microglobulin (beta(2)m)-free and disulfide-linked dimer forms. Notably, LILRB1 cannot recognize the beta(2)m-free form of HLA-G or HLA-B27, but LILRB2 can recognize the beta(2)m-free form of HLA-B27. To date, the structural basis for HLA-G/LILR recognition remains to be examined. Here, we report the 2.5-A resolution crystal structure of the LILRB2/HLA-G complex. LILRB2 exhibits an overlapping but distinct MHCI recognition mode compared with LILRB1 and dominantly recognizes the hydrophobic site of the HLA-G alpha3 domain. NMR binding studies also confirmed these LILR recognition differences on both conformed (heavy chain/peptide/beta(2)m) and free forms of beta(2)m. Binding studies using beta(2)m-free MHCIs revealed differential beta(2)m-dependent LILR-binding specificities. These results suggest that subtle structural differences between LILRB family members cause the distinct binding specificities to various forms of HLA-G and other MHCIs, which may in turn regulate immune suppression.


    Organizational Affiliation

    Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, alpha chain G
A
277Homo sapiensMutation(s): 1 
Gene Names: HLA-G (HLA-6.0, HLAG)
Find proteins for P17693 (Homo sapiens)
Go to Gene View: HLA-G
Go to UniProtKB:  P17693
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
100Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
9 Mer Peptide From Histone H2A.x
C
9Homo sapiensMutation(s): 0 
Gene Names: H2AFX (H2AX)
Find proteins for P16104 (Homo sapiens)
Go to Gene View: H2AFX
Go to UniProtKB:  P16104
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Leukocyte immunoglobulin-like receptor subfamily B member 2
D
196Homo sapiensMutation(s): 0 
Gene Names: LILRB2 (ILT4, LIR2, MIR10)
Find proteins for Q8N423 (Homo sapiens)
Go to Gene View: LILRB2
Go to UniProtKB:  Q8N423
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.233 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 81.400α = 90.00
b = 81.400β = 90.00
c = 186.733γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
CNSrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance