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Figure 1.
Figure 1 Structure of the doubly prenylated Ypt1:GDI complex.
(A) Ribbon representation of GDI (blue) bound to Ypt1 (yellow).
Domain I (dark blue), domain II (light blue), the Rab-binding
platform (red), the C-terminus-binding region (CBR gold) and the
mobile effector loop (MEL green) of GDI are highlighted. The
Switch I and II regions of Ypt1 are highlighted in green and
grey, respectively. The helices composing domain II of GDI are
marked by letters. The isoprenoid moieties 1 (red) and 2 (dark
yellow) are displayed in ball-and-stick representation. The GDP
(atomic colours) and Mg2+ (magenta) ion are shown in the
nucleotide-binding pocket in ball-and-stick and space filling
representations, respectively. Unless otherwise indicated, this
and other figures were prepared using ICM (Molsoft LLC). (B)
Plot of a sigma A-weighted F[o]-F[c] map contoured at 2  (red)
or at 0.6 (black)
in the region of the geranylgeranyl. The maps were generated
after several refinement rounds omitting the GG groups. The
picture was generated with BobScript and RASTER3D (Merritt and
Murphy, 1994; Esnouf, 1997). (C) Domain II of GDI from
Ypt1GG:GDI complex displayed in ribbon representation (grey);
the secondary structure elements are denoted as in (A). The last
visible residues of the Ypt1 C-terminus and of the MEL of GDI
are coloured blue and green, respectively. The geranylgeranyl
moieties 1 (red) and 2 (blue) filling the lipid binding site are
displayed in ball-and-stick representation.
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