6EWA

Crystal structure of HLA-A2 in complex with LILRB1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 

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This is version 1.1 of the entry. See complete history


Literature

Application of the immunoregulatory receptor LILRB1 as a crystallisation chaperone for human class I MHC complexes.

Mohammed, F.Stones, D.H.Willcox, B.E.

(2019) J Immunol Methods 464: 47-56

  • DOI: 10.1016/j.jim.2018.10.011
  • Primary Citation of Related Structures:  
    6EWA, 6EWC, 6EWO

  • PubMed Abstract: 
  • X-ray crystallographic studies of class I peptide-MHC molecules (pMHC) continue to provide important insights into immune recognition, however their success depends on generation of diffraction-quality crystals, which remains a significant challenge. ...

    X-ray crystallographic studies of class I peptide-MHC molecules (pMHC) continue to provide important insights into immune recognition, however their success depends on generation of diffraction-quality crystals, which remains a significant challenge. While protein engineering techniques such as surface-entropy reduction and lysine methylation have proven utility in facilitating and/or improving protein crystallisation, they risk affecting the conformation and biochemistry of the class I MHC antigen binding groove. An attractive alternative is the use of noncovalent crystallisation chaperones, however these have not been developed for pMHC. Here we describe a method for promoting class I pMHC crystallisation, by exploiting its natural ligand interaction with the immunoregulatory receptor LILRB1 as a novel crystallisation chaperone. First, focussing on a model HIV-1-derived HLA-A2-restricted peptide, we determined a 2.4 Å HLA-A2/LILRB1 structure, which validated that co-crystallisation with LILRB1 does not alter conformation of the antigenic peptide. We then demonstrated that addition of LILRB1 enhanced the crystallisation of multiple peptide-HLA-A2 complexes, and identified a generic condition for initial co-crystallisation. LILRB1 chaperone-based crystallisation enabled structure determination for HLA-A2 complexes previously intransigent to crystallisation, including both conventional and post-translationally-modified peptides, of diverse lengths. Since both the LILRB1 recognition interface on the HLA-A2 α3 domain molecule and HLA-A2-mediated crystal contacts are predominantly conserved across class I MHC molecules, the approach we outline could prove applicable to a diverse range of class I pMHC. LILRB1 chaperone-mediated crystallisation should expedite molecular insights into the immunobiology of diverse immune-related diseases and immunotherapeutic strategies, particularly involving class I pMHC complexes that are challenging to crystallise.


    Organizational Affiliation

    Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK. Electronic address: b.willcox@bham.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chainAE276Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
Find proteins for P04439 (Homo sapiens)
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Go to UniProtKB:  P04439
NIH Common Fund Data Resources
PHAROS  P04439
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinBF99Homo 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
PolyproteinCG9Human immunodeficiency virus 1Mutation(s): 0 
EC: 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
LIR-1DH195Homo 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: 2.39 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.15α = 90
b = 116.15β = 90
c = 192.82γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2019-01-16
    Changes: Data collection, Database references