Crystal structure of HLA-G: a nonclassical MHC class I molecule expressed at the fetal-maternal interface

Abstract

HLA-G is a nonclassical major histocompatibility complex class I (MHC-I) molecule that is primarily expressed at the fetal-maternal interface, where it is thought to play a role in protecting the fetus from the maternal immune response. HLA-G binds a limited repertoire of peptides and interacts with the inhibitory leukocyte Ig-like receptors LIR-1 and LIR-2 and possibly with certain natural killer cell receptors. To gain further insights into HLA-G function, we determined the 1.9-A structure of a monomeric HLA-G complexed to a natural endogenous peptide ligand from histone H2A (RIIPRHLQL). An extensive network of contacts between the peptide and the antigen-binding cleft reveal a constrained mode of binding reminiscent of the nonclassical HLA-E molecule, thereby providing a structural basis for the limited peptide repertoire of HLA-G. The alpha3 domain of HLA-G, a candidate binding site for the LIR-1 and -2 inhibitory receptors, is structurally distinct from the alpha3 domains of classical MHC-I molecules, providing a rationale for the observed affinity differences for these ligands. The structural data suggest a head-to-tail mode of dimerization, mediated by an intermolecular disulfide bond, that is consistent with the observation of HLA-G dimers on the cell surface.

Fig. 1.

Overview of the structure of HLA-G. (A) The hc is shown in purple, β₂M in blue, and the peptide in green. The position of the Cys-42 → Ser mutation is labeled. (B) Conformation of bound peptide. The corresponding 2F_o - F_c electron density is shown in mesh format. The peptide is in ball-and-stick format with each amino acid labeled.

Fig. 2.

Sequence alignment of human HLA-G with HLA-E, -A2, -B44, and -CW3 as well as mouse Qa-2. The sequence alignment is divided into the three domains: α1, α2, and α3. Residues highlighted with red have 100% identity. Residues highlighted in yellow are conservatively substituted. The secondary structure of HLA-G is illustrated directly above the sequence alignment. Orange arrows indicate β-strands, and blue cylinders indicate α-helices. Residues directly interacting with the peptide are marked with a large green star, and residues interacting only via a water molecule are marked with a hollow circle (see Table 3). The loop in domain α3 involved in LIR-1/2 (ILT-2/4) binding is highlighted with a green box.

Fig. 3.

Comparison of MHC-I bound peptides. The conformations of peptides bound by HLA-G (purple), HLA-E (48) (red), HLA-A2 (49) (yellow), and Qa-2 (39) (green) are shown in a side view (A), top view (B), and a view showing the main chain interactions between the epitope and the HLA-G hc (C). Polar interactions are depicted only (dashed lines); water molecules are shown in blue spheres.

Fig. 4.

Pocket-mediated interactions of HLA-G. HLA-G residues are shown in purple, peptide residues are shown in green, polar contacts are depicted as dashed lines, and water molecules are shown as blue spheres. (A) Pockets A and B mediating interactions with P1-Arg and P2-Ile, respectively. (B) Pockets C and D mediating interactions with P6-His and P2-Pro, respectively. (C) Pockets E and F mediating interactions with P7-Leu and P9-Leu, respectively. (D) Overview of the hydrophobic nature of the HLA-G binding cleft. Hydrophobic regions of the cleft that bind peptide are shown in green with the important anchor residue His-70 colored yellow. The pockets are labeled A–F, and the peptide is depicted as a ball-and-stick structure.

Fig. 5.

HLA-G may bind to LIR-1 (ILT-2) with enhanced affinity and undergo disulfide-bond-mediated dimerization. (A) Comparative analysis of the candidate ILT-2 binding site on the α3 domain of HLA-G (purple) and the equivalent binding site on HLA-A2 (yellow). (B) Model of the HLA-G dimer, looking down onto the antigen-binding cleft; peptides are in red (A protomer, light gray) and pink (B protomer, dark gray). The dimerization site is mediated via an intermolecular Cys-42–Cys-42 disulfide, indicating that the protomers within the dimer cannot adopt a side-by-side arrangement. However, a head-to-tail HLA-G dimer would satisfy the requirements for a Cys-42-mediated dimer, in which the loops containing the Cys-42 would clasp onto each other. In this plausible configuration, intermolecular interactions mediated via the β2M domains are possible. LIR-1 has been solved in complex with HLA-A2 (Protein Data Bank ID code 1P7Q), in which the LIR-1 binding site onto the α3 domain of the hc was mapped. Given the similarities between HLA-G and HLA-A2, the molecular organization of the HLA-G/ILT2 complex can be postulated in this HLA-G dimeric arrangement (ILT2 in blue and cyan).