Alignment of structures of two Ran proteins. (a) Structure of human Ran (cartoon) bound to a non-hydrolysable GTP analogue (sticks) with the Ran-binding domain of human RanBP2 (grey surface). The SWITCH I and II loops are shown in red, the C-terminal helix is displayed in orange. (b) Structure of a Q69L mutant of canine Ran (cartoon) with a bound GDP molecule (sticks) (c) Superposition of the two Ran molecules on the first rigid body identified by RAPIDO (140 atoms, RMSD 0.76 Å). The different conformations of the SWITCH I and II fragments as well as the large displacement of the C-terminal helix are clearly visible. In this figure (and in all other figures), the first rigid body is colored in blue, the second in green, the third in cyan, the fourth in magenta. Parts of structures that cannot be aligned are marked in grey. Parts of structures that were aligned and then identified as having different conformations in different structures are colored red. When two structures are compared, one is shown in light, the other in dark colors – here the structure of the protein from human is shown in dark colors, while the structure from dog is shown in light colors. (d) Superposition of the two Ran molecules on the second rigid body consisting mostly of the C-terminal helix (in green, 18 atoms, RMSD 1.35 Å). The unstructured linker preceding the C-terminal helix has been found to be flexible and is marked red. All figures were produced with PyMOL http://pymol.sourceforge.net/.