1. Volume 11, Issue 2, Pages 483-494 (February 2003)
Structure of Rab Escort Protein-1 in Complex with Rab Geranylgeranyltransferase 
Olena Pylypenko, Alexey Rak, Reinhard Reents, Anca Niculae, Vadim Sidorovitch, Maria-Daniela Cioaca, Ekaterina Bessolitsyna, Nicolas H Thomä, Herbert Waldmann, Ilme Schlichting, Roger S Goody, Kirill Alexandrov 
Molecular Cell 
Volume 11, Issue 2, Pages (February 2003)
DOI: /S (03)

2. Figure 1 Overview of RabGGTase:REP-1 Complex
(A) Ribbon diagram of the RabGGTase/farnesyl/Zn2+/REP-1 complex. The α subunit of RabGGTase is shown in green, the β subunit in gray, LRR domain in pink, and Ig-like domain in orange. Domain I of REP-1 is shown in dark blue, while domain II is in light blue, farnesyl in ball and stick representation in red, and Zn2+ as a magenta ball. The helices of the α subunit of RabGGTase are labeled in Greek letters followed by a number. The helices of domain II and helix M of the domain I of REP-1 are labeled in capital letters. Unless otherwise indicated, this and other figures were prepared using ICM 2.8 (Molsoft LLC).
(B) Ball and stick representation of the phosphoisoprenoid binding pocket of RabGGTase with farnesyl molecule (blue), zinc ion (green), and a putative peptide (atomic colors). Key residues in the lipid binding site are marked.
(C) Surface representation of the phosphoisoprenoid binding site of RabGGTase superimposed with the FTase bound to a farnesyldiphosphate analog and a substrate peptide (PDB code 1D8D). The farnesyl residue found in the structure of RabGGTase is shown in blue, the farnesyldiphosphate analog in FTase in atomic colors, the FTase substrate peptide in green, and the putative peptide of RabGGTase in dark blue. The surface is colored according to electrostatic potential, with blue representing regions of positive potential and red regions of negative potential. Zinc ions of RabGGTase and FTase are shown as green and magenta balls, respectively.
Molecular Cell  , DOI: ( /S (03) )

3. Figure 2 Comparison of REP-1 and RabGDI Structures
Ribbon diagrams of REP-1 (A) and αRabGDI (B). Superposition of the Cα atoms of REP-1 and αRabGDI resulted in an rmsd of 3.2 Å. The structural elements of REP-1 absent in RabGDI are shown in green. Green arrows bridging the chain breaks indicate the approximate position of disordered fragments. The Rab binding platforms of REP-1 and RabGDI are highlighted in red and the effector loops in blue. The secondary structure assignment was determined using the program ICM, and the GDI nomenclature was used for the structural description of REP-1. Helices are labeled alphabetically according to their appearance in the sequence; β sheets are labeled in lower case, with numbers designating their order in the sequence.
Molecular Cell  , DOI: ( /S (03) )

4. Figure 3 RabGGTase:REP-1 Interface
(A) Ball and stick representation of the RabGGTase:REP-1 interface. REP-1 is displayed in green and RabGGTase in gray. The oxygens and nitrogens are colored red and blue, respectively. The hydrogen bonds were calculated with ICM and are displayed as blue dotted lines.
(B) REP-1 binding site on the RabGGTase in surface representation. The surface was calculated in the 7 Å vicinity of the REP-1 molecule and colored according to charge. Helices D and E are displayed as green worms, and residues of REP-1 within 3.5 Å distance of RabGGTase are displayed in ball and stick representation.
(C) Ribbon representation of α subunits of apo-RabGGTase and RabGGTase in complex with REP-1. Apo-RabGGTase molecule a is in gray, molecule b is in blue, and RabGGTase in complex with REP-1 is in red. The Phe 279 of REP-1 is represented in ball and stick in green.
(D) Ball and stick representation of superimposed helices E and D of αRabGDI (gray) with helices E and D of REP-1 (green) in complex with RabGGTase (displayed as molecular surface). Nonconserved residues are labeled in white.
Molecular Cell  , DOI: ( /S (03) )

5. Figure 4
Family-Specific and Generic Features of RabGGTase:REP-1 Interface
(A) Multiple sequence alignment of domains II of REP and RabGDI from various organisms. Invariant residues are shown in black, conserved residues in blue. The phenylalanine residues of domain II are shown in red. The position of conserved phenylalanines specific for REP and RabGDI families are marked by arrows.
(B) B factors of α subunits of apo-RabGGTase and RabGGTase in complex with REP-1. B factors of residues of Apo-RabGGTase molecules: molecule a plotted in black, molecule b in blue, and RabGGTase in complex with REP-1 in red. The reduction in B factors of the Ig domain in the complex is due to the crystallographic contact.
(C–E) Protein:protein binding interfaces with structural similarity to the RabGGTase:REP-1 binding interface depicted in surface representation. The surface was calculated in the 7 Å vicinity of the second molecule and colored according to charge. (C) RabGGTase:REP-1 complex, where RabGGTase is displayed as a molecular surface. (D) gp120:CD4 complex, where gp120 is displayed as a molecular surface. (E) Thrombin complexed with fibrinopeptide A, where thrombin is displayed as a molecular surface.
Molecular Cell  , DOI: ( /S (03) )

6. Figure 5
Regulation of RabGGTase:REP-1 Complex Formation by Phosphoisoprenoids
(A) The residues of RabGGTase potentially involved in signal transduction to the REP binding site on the α subunit of RabGGTase in ball and stick representation. The farnesyl moiety is shown in green, βR144 of the molecule a of apo-RabGGTase is shown in orange, and the residues βR144 (molecule b) and αY107 are shown in atomic colors. Parts of the β subunit are shown in gray ribbon, while the α subunit of RabGGTase is shown in red ribbon. The rF279 of REP-1 is shown in ball and stick representation and marked by a red arrow.
(B) Detection of the RabGGTase:GGPP:REP-1 complex by affinity precipitations. Precipitation experiments were performed with 6× His-tagged REP-1 bound to Ni-NTA-agarose incubated with the wild-type or αY107A mutant RabGGTase. After incubation, the samples were washed with the incubation buffer, and aliquots of the pellet were analyzed by 15% SDS-PAGE, followed by Coomassie blue staining.
(C) Fluorescence titration of the RabGGTase:mFPP (open circles) or the RabGGTase_αY107A:mFPP (closed circles) complex (200 nM) versus increasing concentrations of REP-1. The experimental curve was fitted to give a Kd value of 24 ± 0.6 nM.
(D) Interaction of RabGGTase with F279A mutant of REP-1 by affinity precipitations. Precipitation experiments were performed as in (B).
Molecular Cell  , DOI: ( /S (03) )

7. Figure 6 Model of Ternary RabGGTase:REP-1:Rab3a Complex
(A) Model of the quaternary RabGGTase:Fpcp:REP-1:Rab3a complex generated by docking of Rab3a onto the RabGGTase:Fpcp:REP-1 complex. The α subunit of RabGGTase is shown in green, the β subunit in gray, the domain I of REP-1 is in dark blue, domain II in light blue, the effector loop of REP-1 in yellow, and the Rab binding platform in gold. Rab3a is shown in red, Fpcp is shown in ball and stick representation in orange, and Zn2+ as a magenta ball. The C terminus of Rab3a docked into the active site of RabGGTase is shown in red, while the alternative conformation with the C terminus docked to the putative lipid binding site on REP-1 is shown in pink.
(B) Surface representations of RabGGTase with the C terminus of Rab3a protruding into the active site. Fpcp is shown in ball and stick representation in blue.
(C) Surface representations of REP-1. The Rab binding platform is colored black, the REP effector loop orange, and the putative lipid binding site is red. The putative position of the second lipid binding site is indicated by arrows.
(D) The model rotated by 90° with the double geranylgeranylated C terminus of Rab3a docked into it. Hydrophobic amino acids are colored red, residues of the REP effector domain orange, isoprenoid moieties blue, and Rab3a is represented as a yellow worm.
Molecular Cell  , DOI: ( /S (03) )