Structural basis of malaria RIFIN binding by LILRB1-containing antibodies

We previously reported that certain Plasmodium falciparum RIFINs, variant surface antigens expressed on infected erythrocytes(1), bind to the inhibitory receptor LAIR1 and insertions of DNA encoding LAIR1 into immunoglobulin genes generate RIFIN-specific antibodies(2,3). To address the general relevance of this finding, we searched for antibodies that incorporate LILRB1, another inhibitory receptor that binds to β2 microglobulin and RIFINs through their apical domains(4,5). By screening plasma from a Malian cohort, we identified individuals with LILRB1-containing antibodies. B cell clones isolated from three donors showed large DNA insertions in the switch region encoding non-apical LILRB1 D3D4 or D3 alone in the variable-constant (VH-CH1) elbow. Through mass-spectrometry and binding assays, we identified a large set of RIFINs that bind to LILRB1 D3. The crystal and cryo-EM structures of a RIFIN in complex with either LILRB1 D3D4 or a D3D4-containing antibody Fab revealed a mode of RIFIN-LILRB1 D3 interaction comparable to that of RIFIN-LAIR1 (Xu et al, in press). Remarkably, the Fab showed an unconventional triangular architecture with the inserted LILRB1 domains opening up the VH-CH1 elbow without affecting VH-VL nor CH1-CL pairing. Collectively, these findings identify a new modality of RIFIN binding to LILRB1 through D3 and illustrate, with a naturally selected example, the general principle of creating novel antibodies by inserting receptor domains in the VH-CH1 elbow.