Fig. 3: The SDII-SDII‘ interface allows for motion between GephE dimers.
From: Gephyrin filaments represent the molecular basis of inhibitory postsynaptic densities
a Overlay of the alternative SDII‘ binding position (orange) within the SDII-SDII‘ interface with the main position observed for SDII‘ in the interface (green). For orientation, SDI and SDII of one GephE subunit (light blue), and SDII and SDIV of the second GephE monomer (dark blue) in the dimer are shown. The shift between the SDII‘ positions is indicated. For further information, see Supplementary Fig. 8. Scale bar is 25 Å. b, c Visualization of main trajectories depicting possible degrees of freedom of SDII (blue) and SDII‘ (green or orange) in the main (b) and alternative (c) binding positions based on motion-based deep generative modeling. Strongest deviation from the consensus position is highlighted in color, the course of movement shown in shades of gray, and the difference between the extreme positions indicated in degrees. For further information see Supplementary Figs. 8 and 9d–g) Structural comparison of the SDII position in the GephE dimer incorporated into filaments in the presence of GlyR-loop (blue) with the crystal structure without GlyR-loop (PDB: 2FU3, olive (d), the GephE crystal structure bound to GlyR-loop (PDB: 2FTS, red (e), the Cnx1E crystal structure without Moco-AMP (PDB: 5G2R, dark orange (f), and the Cnx1E crystal structure bound to Moco-AMP (PDB: 6Q32, purple (g). Differences in SDIIs positions are indicated in distances and angular changes. For further information, see Supplementary Fig. 9.
