Fig. 5
Structural analysis of GABARAP-PCM1 peptide complex. a Density plot for the conformations of PCM1 LIR in the GABARAP binding pocket, sampled during simulations starting from the bent (in yellow) and extended (in orange) conformations. The plot illustrates the similarity of the PCM1 LIR (light blue cartoon) conformations (measured as all-atom RMSD) with respect to each of the two initial structures for the simulations in complex with GABARAP (i.e., the bent and the extended conformation in yellow and orange cartoons, respectively). Starting from different conformations, the simulations of the PCM1 LIR into the GABARAP pocket converge on a similar ensemble of bent structures. b The common ensemble of bent structures of the PCM1 LIR peptide and ten representative conformations were isolated and are shown as a light blue cartoon. As a comparison, ten structures of the PCM1 LIR peptide from the simulations in complex with LC3B were reported and are indicated as dark blue cartoon. c Pairwise intermolecular contacts between residues of GABARAP and PCM1 LIR peptide were estimated in the selected ensemble. Contacts are represented as red cylinders connecting the Cα atoms of the pair of residues involved in the interaction. The radius of each cylinder is proportional to the occurrence of the contact, e.g. a contact presents in all structures of the selected ensemble has a radius of 0.5 Å. We here report the most important residues of GABARAP (yellow cartoon, E8, H9, K20, K46, K47, K48, and Y25) for the interaction between the 1959-DEED-1962 and K1965 of PCM1-LIR (light blue cartoon). The residues selected for experimental mutagenesis are circled and their Cα atoms are shown as spheres. d GFP-precipitation of GFP-3xFLAG or GFP-tagged GABARAP-wt or the indicated mutants in HEK293 cells analyzed for co-precipitation of endogenous PCM1, n = 2. e GST pull-down of GST, GST-GABARAP-wt or the indicated mutant analyzed for co-precipitation of endogenous PCM1, in HEK293 cells, n = 2. f GST pull-down of GST, GST-LC3B-wt or the indicated mutants analyzed for co-precipitation of endogenous PCM1, in HEK293 cells, n = 2
