3Q2C | pdb_00003q2c

Binding properties to HLA class I molecules and the structure of the leukocyte Ig-like receptor A3 (LILRA3/ILT6/LIR4/CD85e)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.257 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

LILRA3 binds both classical and non-classical HLA class I molecules but with reduced affinities compared to LILRB1/LILRB2: structural evidence

Ryu, M.Chen, Y.Qi, J.Liu, J.Fan, Z.Nam, G.Shi, Y.Cheng, H.Gao, G.F.

(2011) PLoS One 6: e19245-e19245

  • DOI: https://doi.org/10.1371/journal.pone.0019245
  • Primary Citation Related Structures: 
    3Q2C

  • PubMed Abstract: 

    Structurally, Group 1 LILR (Leukocyte Immunoglobulin (Ig)-Like Receptor, also known as Ig-like transcripts, ILT; Leukocyte Ig-like receptor, LIR; and CD85) members are very similar in terms of the HLAIs (human leukocyte antigen class I molecules) binding region and were hypothesized that they all bind to HLAIs. As one of the Group 1 LILRs, LILRA3 is the only secretory LILR and may greatly control the inhibitory immune response induced by LILRB1, LILRB2, and other HLA-binding LILR molecules like LILRA1. Nevertheless, little was known about the binding of LILRA3 to HLAIs. In this report, we present the crystal structure of the LILRA3 domain 1 (D1) and evaluate the D1 and D1D2 (domain 1 and domain 2) binding to classical and non-classical HLAIs using BIAcore® surface plasmon resonance analysis (SPR). We found that LILRA3 binds both classical HLA-A*0201 and non-classical HLA-G1 but with reduced affinities compared to either LILRB1 or LILRB2. The polymorphic amino acids and the LILRA3 D1 structure support this notion.


  • Organizational Affiliation
    • CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 10.79 kDa 
  • Atom Count: 787 
  • Modeled Residue Count: 96 
  • Deposited Residue Count: 97 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Leukocyte immunoglobulin-like receptor subfamily A member 397Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q8N6C8 (Homo sapiens)
Explore Q8N6C8 
Go to UniProtKB:  Q8N6C8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N6C8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.257 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.308α = 90
b = 27.817β = 111.65
c = 48.257γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-13
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-30
    Changes: Structure summary