6K60

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 

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
  • Structures With Same Primary Citation

  • 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.



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-GHLA-6.0HLAG
Find proteins for P17693 (Homo sapiens)
Go to UniProtKB:  P17693
NIH Common Fund Data Resources
PHAROS  P17693

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, F
100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Peptide from Histone H2A.J
C, G
9Homo sapiensMutation(s): 0 
Find proteins for A0A0U1RRH7 (Homo sapiens)
Go to UniProtKB:  A0A0U1RRH7

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Leukocyte immunoglobulin-like receptor subfamily B member 1
D, H
198Homo sapiensMutation(s): 0 
Gene Names: LILRB1
Find proteins for A0A0G2JQ44 (Homo sapiens)
Go to UniProtKB:  A0A0G2JQ44
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

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: 3.15 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.378α = 90
b = 164.378β = 90
c = 326.839γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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
    Changes: Database references