Fig. 4

Example of a complex structural re-arrangement. Structural superposition with MOMA of proteins Sec31 of the COPII complex of coat vesicle (the query; PDB code 2QX5, chain A) and the nucleoporin Nic96 (the target; PDB code 2PM7, chain A). Top Panel: The structure matching domains are shown in the alignment of SSEs and the respective sub-matrices surrounded by red, blue and green colored boxes. Bottom Panel: The three independent protein structure sectors that match between the two proteins, identified by MOMA, are highlighted by green, orange and blue colored boxes (Bottom Left). The alignment of SSE pairs and the independent structural superposition of the three matching block pairs are shown in red-orange, cyan-blue and light–dark green colours (Bottom Right). In this example MOMA was executed with the following parameters: g1 = −5, g2 = −5 and C = 45