3D Domain Swap Systems - ProSwap - Wodak Lab

3D domain-swapped systems are characterized by the interconversion between ‘closed’ monomeric proteins and an intertwined homo-oligomer, where specific intramolecular contacts are substituted for their intermolecular equivalents (Bennett et al., 1994; Bennett et al., 1995; Liu and Eisenberg, 2002). These systems involve the exchange of structural domains as well as chain segments that do not correspond to such domains.

Here we list 115 3D domain-swapped systems identified from the PDB (January 2011 snapshot) using automatic procedures. These procedures identify pairs of monomer and homo-oligomers with the same or related sequences, where the non-contiguous structural domain in the oligomer is similar enough to the structure of the monomer (see MacKinnon et al. 2012).

In some cases, such as RNase A, multiple 3D domains swapped systems are reported for the same protein family. In rare cases, such as the prion protein, two separate entries are provided for seemingly similar swaps, because the protein sequences in these entries differ significantly in length, which resulted in assigning them to distinct sequence families.