Fig. 3

CryoEM and structural analysis of an RPA dimer on ssDNA. a, b 3D reconstruction of yeast RPA dimer subclass at sub-nanometer resolution (7.5 Å by gold standard-FSC). The models fitted in the 4.7 Å maps (colored as in Fig. 2) are fitted into the density corresponding to the Tri-C. Additional density not described by the fitted of the models. A 2D class average of a similar view is shown alongside (a). c, d The atomic co-ordinates Rpa14, DbdA/DbdB, and the associated ssDNA were excised from pdb: 4GOP and aligned by secondary structure onto DBD-E. The positions of DBD-A and DBD-B, relative to Rpa14 (aligned on DBD-E), are in similar positions to the additional density unaccounted for by either Tri-C. d The 5′ and 3′ ends of the ssDNA in each model are labeled to indicate that ssDNA could pass from DBD-A to the Tri-C. e, f DBD-A and DBD-B of the fungal structure from c, d are replaced with the yeast DBD-A NMR structure (pdb 1YNX) and a Phyre2-generated DBD-B homology model by superposition. DBD-B, which is slightly out of the density, is adjusted slightly by fitted as a rigid body in Chimera. The density for DBD-A is slightly weaker than DBD-B, suggesting that even in this subclass there is some occupancy heterogeneity