6AED

Crystal Structure of the four Ig-like domain of LILRB2(LIR2/ILT4/CD85d)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.265 

wwPDB Validation   3D Report Full Report


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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:  
    6AED, 6AEE

  • 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. 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 ...

    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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Leukocyte immunoglobulin-like receptor subfamily B member 2A396Homo sapiensMutation(s): 1 
Gene Names: LILRB2ILT4LIR2MIR10
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N423 (Homo sapiens)
Explore Q8N423 
Go to UniProtKB:  Q8N423
PHAROS:  Q8N423
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N423
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.265 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.196α = 90
b = 172.196β = 90
c = 65.602γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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