A recently discovered family of Membrane‑Associated RING-CH (MARCH) E3 ligases regulates the cell‑surface expression of a wide array of immunologically important membrane proteins through the attachment of the small cytosolic protein ubiquitin. Ubiquitination leads to redistribution of target membrane proteins into intracellular compartments and increased endosomal and/or proteasomal degradation. Two viral E3 ligases termed Modulator of Immune Recognition 1 and 2 (MIR1/2) and six homologous mammalian MARCH E3 ligases target an overlapping set of cell surface proteins including the antigen presenting major histocompatibility complex (MHC) class I and class-II molecules, the T‑cell co‑stimulatory receptor CD86, the cell-adhesion protein ICAM-1, the T‑cell co‑receptor CD4 and the interleukin‑1 receptor accessory protein. MIR and MARCH proteins share a catalytically active N-terminal PHD/RING-CH domain followed by two transmembrane (TM) domains and a C-terminal tail. Domain-swap experiments suggest that the MIR and MARCH TM-Loop-TM sequences encode substrate preference and specifically recognise substrate TM regions. To define the amino acid sequences and structural features that drive this unusual mode of intramembrane molecular recognition, we aim determine TM domain structures of several MARCH and MIR E3 ligases and of the complexes they form with substrates through crystallisation of TM peptides in lipidic cubic phase media.  The sequence dependence of TM-TM interactions will further be characterised by applying an in vitro Förster Resonance Energy Transfer (FRET) assay using purified peptides reconstituted in liposomes. Understanding the structural basis of substrate recognition could provide a valuable tool for rational design of therapeutics to counteract viral immune evasion and/or to enhance efficacy of vaccines and cancer immunotherapies.