6K60

Structural and functional basis for HLA-G isoform recognition of immune checkpoint receptor LILRBs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.149 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Functional Basis for LILRB Immune Checkpoint Receptor Recognition of HLA-G Isoforms.

Kuroki, K.Matsubara, H.Kanda, R.Miyashita, N.Shiroishi, M.Fukunaga, Y.Kamishikiryo, J.Fukunaga, A.Fukuhara, H.Hirose, K.Hunt, J.S.Sugita, Y.Kita, S.Ose, T.Maenaka, K.

(2019) J Immunol. 203: 3386-3394

  • DOI: 10.4049/jimmunol.1900562

  • PubMed Abstract: 
  • Human leukocyte Ig-like receptors (LILR) LILRB1 and LILRB2 are immune checkpoint receptors that regulate a wide range of physiological responses by binding to diverse ligands, including HLA-G. HLA-G is exclusively expressed in the placenta, some immu ...

    Human leukocyte Ig-like receptors (LILR) LILRB1 and LILRB2 are immune checkpoint receptors that regulate a wide range of physiological responses by binding to diverse ligands, including HLA-G. HLA-G is exclusively expressed in the placenta, some immunoregulatory cells, and tumors and has several unique isoforms. However, the recognition of HLA-G isoforms by LILRs is poorly understood. In this study, we characterized LILR binding to the β2-microglobulin (β2m)-free HLA-G1 isoform, which is synthesized by placental trophoblast cells and tends to dimerize and multimerize. The multimerized β2m-free HLA-G1 dimer lacked detectable affinity for LILRB1, but bound strongly to LILRB2. We also determined the crystal structure of the LILRB1 and HLA-G1 complex, which adopted the typical structure of a classical HLA class I complex. LILRB1 exhibits flexible binding modes with the α3 domain, but maintains tight contacts with β2m, thus accounting for β2m-dependent binding. Notably, both LILRB1 and B2 are oriented at suitable angles to permit efficient signaling upon complex formation with HLA-G1 dimers. These structural and functional features of ligand recognition by LILRs provide novel insights into their important roles in the biological regulations.


    Organizational Affiliation

    Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan; maenaka@pharm.hokudai.ac.jp.,Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.,RIKEN, Kobe 650-0047, Japan.,Department of Computational Systems Biology, Kindai University, Kinokawa 649-6493, Japan.,Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan.,Faculty of Pharmaceutical Sciences, Fukuyama University, Fukuyama 729-0292, Japan; and.,Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, alpha chain G
A, E
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, F
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
Peptide from Histone H2A.J
C, G
9Homo sapiensMutation(s): 0 
Gene Names: H2AFJ
Find proteins for Q9BTM1 (Homo sapiens)
Go to Gene View: H2AFJ
Go to UniProtKB:  Q9BTM1
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Leukocyte immunoglobulin-like receptor subfamily B member 1
D, H
198Homo sapiensMutation(s): 0 
Gene Names: LILRB1 (ILT2, LIR1, MIR7)
Find proteins for Q8NHL6 (Homo sapiens)
Go to Gene View: LILRB1
Go to UniProtKB:  Q8NHL6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A, B, C, E, G
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.149 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.261 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 164.378α = 90.00
b = 164.378β = 90.00
c = 326.839γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)Japan18am0101093j0002
Japan Society for the Promotion of ScienceJapan23770102
Japan Society for the Promotion of ScienceJapan25870019

Revision History 

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2019-12-25
    Type: Database references