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 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.4049/jimmunol.1900562
  • Primary Citation of Related Structures:  
    6K60

  • 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 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, alpha chain G
A, E
277Homo sapiensMutation(s): 1 
Gene Names: HLA-GHLA-6.0HLAG
UniProt & NIH Common Fund Data Resources
Find proteins for P17693 (Homo sapiens)
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Go to UniProtKB:  P17693
PHAROS:  P17693
GTEx:  ENSG00000204632 
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UniProt GroupP17693
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, F
100Homo sapiensMutation(s): 0 
Gene Names: B2M
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
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PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide from Histone H2A.J
C, G
9Homo sapiensMutation(s): 0 
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PHAROS:  Q9BTM1
GTEx:  ENSG00000246705 
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UniProt GroupQ9BTM1
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Leukocyte immunoglobulin-like receptor subfamily B member 1
D, H
198Homo sapiensMutation(s): 0 
Gene Names: LILRB1
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Find proteins for Q8NHL6 (Homo sapiens)
Explore Q8NHL6 
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PHAROS:  Q8NHL6
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UniProt GroupQ8NHL6
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  • Reference Sequence
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

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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  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary