Effectors of Rab GTPases: Rab Binding Specificity and Their Role in Coordination of Rab Function and Localization - Ras Superfamily Small G Proteins: Biology and Mechanisms 2 - page 45

Fig. 3.3 Interaction sites of different Rab binding proteins. Surface representation of Rab proteins
illustrating the interacting residues within complex structures. The interaction sites of a Rab:
effector, Rab:GEF, and Rab:GAP interaction and of GDI and REP are shown in green . All Rab
residues that contain atoms that are within 5 of an effector atom were considered to be part of the

interaction site. The Rab8:Rabin8 structure was chosen as an example of a Rab:GEF structure
[PDB ID 4LHZ (Hou et al. 2011 )]. The GAP interaction was taken from the Rab1b:TBC1D20
structure [PDB ID 4HLQ (Gavriljuk et al. 2012 )]. The Rab7:REP [PDB ID 1VG0 (Rak
et al. 2004 )] and the Ypt1:GDI structure [PDB ID 2BCG (Pylypenko et al. 2006 )] were used to
represent the interactions of REP and GDI. In comparison to the other interactions the interactions
with REP and GDI show a second interaction area that represents the C-terminal region of the Rab
proteins

Å

in the published complexes [performed with ClustalX (Larkin et al. 2007 )]. In
Fig. 3.4 , the interacting residues on the Rab proteins are colored according to their
conservation within this alignment. It can be seen that all Rab proteins recognize