6AEE

Crystal structure of the four Ig-like domains of LILRB1 complexed with HLA-G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

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Literature

Structures of the four Ig-like domain LILRB2 and the four-domain LILRB1 and HLA-G1 complex.

Wang, Q.Song, H.Cheng, H.Qi, J.Nam, G.Tan, S.Wang, J.Fang, M.Shi, Y.Tian, Z.Cao, X.An, Z.Yan, J.Gao, G.F.

(2019) Cell Mol Immunol 

  • DOI: 10.1038/s41423-019-0258-5
  • Primary Citation of Related Structures:  
    6AEE, 6AED

  • PubMed Abstract: 
  • Leukocyte immunoglobulin (Ig)-like receptors (LILRs), also known as CD85 and immunoglobulin-like transcripts (ILTs), play pivotal roles in regulating immune responses. These receptors define an immune checkpoint that immune therapy can target. Throug ...

    Leukocyte immunoglobulin (Ig)-like receptors (LILRs), also known as CD85 and immunoglobulin-like transcripts (ILTs), play pivotal roles in regulating immune responses. These receptors define an immune checkpoint that immune therapy can target. Through cis or trans interactions with human leukocyte antigen (HLA)-G, the two most abundantly expressed inhibitory LILRs, LILRB1, and LILRB2 (LILRB1/2, also known as CD85j/d and ILT2/4), are involved in immunotolerance in pregnancy and transplantation, autoimmune diseases, and immune evasion by tumors. Although the discrete domains of LILRB1/2 are clear, the assembly mode of the four extracellular Ig-like domains (D1, D2, D3, and D4) remains unknown. Previous data indicate that D1D2 is responsible for binding to HLA class I (HLA-I), but the roles of D3D4 are still unclear. Here, we determined the crystal structure of the four Ig-like domain LILRB2 and four-domain LILRB1 in complex with HLA-G1. The angles between adjacent domains and the staggered assembly of the four domains suggest limited flexibility and limited plasticity of the receptors during ligand binding. The complex structure of four-domain LILRB1 and HLA-G1 supports the model that D1D2 is responsible for HLA-I binding, while D3D4 acts as a scaffold. Accordingly, cis and trans binding models for HLA-I binding to LILRB1/2 are proposed. The geometries of LILRB1/2 in complex with dimeric and monomeric HLA-G1 suggest the accessibility of the dimeric receptor, which in turn, transduces more inhibitory signals. The assembly of LILRB1/2 and its binding to HLA-G1 could aid in the design of immune regulators and benefit immune interference.


    Organizational Affiliation

    National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), 102206, Beijing, China. gaof@im.ac.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, alpha chain GAD277Homo sapiensMutation(s): 3 
Gene Names: HLA-GHLA-6.0HLAG
Find proteins for P17693 (Homo sapiens)
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PHAROS  P17693
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinBE100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
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PHAROS  P61769
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
9 Mer Peptide (RL9) From Histone H2A.xCF9Homo sapiensMutation(s): 0 
Gene Names: H2AC4H2AFMHIST1H2ABH2AC8H2AFAHIST1H2AE
Find proteins for P04908 (Homo sapiens)
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PHAROS  P04908
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Leukocyte immunoglobulin-like receptor subfamily B member 1GH399Homo sapiensMutation(s): 0 
Gene Names: LILRB1ILT2LIR1MIR7
Find proteins for Q8NHL6 (Homo sapiens)
Explore Q8NHL6 
Go to UniProtKB:  Q8NHL6
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PHAROS  Q8NHL6
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.683α = 90
b = 154.681β = 102.24
c = 98.198γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-07-31
    Type: Initial release