PDBsum entry 6ewc

Immune system

PDB id: 6ewc

Contents

Protein chains

276 a.a.

99 a.a.

186 a.a.

Ligands

ARG-LEU-SER-SER-PRO-LEU-HIS-PHE-VAL ×2

PDB id:

6ewc

Name:

Immune system

Title:

Crystal structure of non-phosphorylated form of rls phosphopeptide bound to hla-a2 in complex with lilrb1

Structure:

Hla class i histocompatibility antigen, a-2 alpha chain. Chain: a, e. Synonym: mhc class i antigen a 2. Engineered: yes. Beta-2-microglobulin. Chain: b, f. Engineered: yes. Reticulophagy regulator 2. Chain: c, g.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hla-a, hlaa. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: plyss. Gene: b2m, cdabp0092, hdcma22p. Synthetic: yes.

Resolution:

3.20Å R-factor: 0.208 R-free: 0.246

Authors:

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

Key ref:

F.Mohammed et al. (2019). Application of the immunoregulatory receptor LILRB1 as a crystallisation chaperone for human class I MHC complexes. J Immunol Methods, 464, 47-56. PubMed id: 30365927 DOI: 10.1016/j.jim.2018.10.011

Date:

03-Nov-17 Release date: 07-Nov-18

Protein chains

P04439  (1A03_HUMAN) -  HLA class I histocompatibility antigen, A alpha chain from Homo sapiens

Seq: 365 a.a.

Struc: 276 a.a.*

Protein chains

P61769  (B2MG_HUMAN) -  Beta-2-microglobulin from Homo sapiens

Seq: 119 a.a.

Struc: 99 a.a.

Protein chains

Q8NHL6  (LIRB1_HUMAN) -  Leukocyte immunoglobulin-like receptor subfamily B member 1 from Homo sapiens

Seq: 650 a.a.

Struc: 186 a.a.*

* PDB and UniProt seqs differ at 23 residue positions (black crosses)

DOI no: 10.1016/j.jim.2018.10.011

J Immunol Methods 464:47-56 (2019)

PubMed id: 30365927

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

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

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. 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.