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. 2020 Jun 8;9:e54434. doi: 10.7554/eLife.54434

Figure 1. Rab5 backbone dynamics during nucleotide exchange.

(A) Scheme of reaction. The ternary complex (Rab5/Rabex5/Rabaptin5) was incubated in D2O for 1, 5 or 15 min in the presence or absence of GTPγS. (B) Crystal structure of Rab5:GTP (PDBID: 3MJH) pseudocolored to show differential uptake of ternary complex (Rab5/Rabex5/Rabaptin5)±GTPγS (average of 1 min, 5 min and 15 min timepoints). The Mg2+ ion is shown as a sphere (magenta) and GTPγS as a line structure. Color scheme: regions that are protected from exchange, i.e. stabilization, are colored with cool colors; regions with enhanced exchange with warm colors; regions with no statistically different uptake are colored in grey; and regions with no peptide coverage are white. (C) Deuterium incorporation over time in Rab5 β2 (aa 58–63, colored blue in B), in the ternary complex (Rab5/Rabex5/Rabaptin5)±GTPγS (n = 3) (D) Differential deuterium incorporation in Rabaptin5 during the nucleotide exchange reaction. Two areas of protection (decrease in deuterium uptake) correspond with the Rab5 binding sites.

Figure 1.

Figure 1—figure supplement 1. Differential deuterium uptake of Rab5 and Rabaptin5 during nucleotide exchange.

Figure 1—figure supplement 1.

(A) Differential uptake of Rab5 in the ternary complex (Rab5/Rabex5/Rabaptin5)±GTPγS (average of 1 min, 5 min and 15 min timepoints). See also Figure 1B. (B) Differential uptake of Rabaptin5 in the ternary complex (Rab5/Rabex5/Rabaptin5)±GTPγS (average of 1 min, 5 min and 15 min timepoints). See also Figure 1D.