Figure 3
From: Molecular architecture of the Ub-PCNA/Pol η complex bound to DNA

Structure of the native Ub-PCNA exhibits a conformation different from that of the Ub-PCNA bound to Pol η and DNA.
(a) Top and bottom views of 3D reconstruction of with the fitted split-fusion Ub-PCNA crystal structure (light blue; PDB ID 3L0W). Scale bar represents 25 Å. (b) Bottom view of (a) but with ubiquitin (yellow; PDB ID 1UBQ) independently fitted into the map. The different orientation of the ubiquitins observed between the two structures suggests local flexibility. (c) Close-up views of the two ubiquitins overlaid. The orientation of the ubiquitin (yellow) fitted according to the native Ub-PCNA EM map exposes the hydrophobic residues (magenta; Leu8, Ile44, Val70) necessary for its interaction with UBD. The same hydrophobic residues on ubiquitin (semi-transparent light blue) in the split-fusion crystal structure are colored green. Left, end-on view towards to the central symmetry axis of PCNA; Right, 90° rotation of the end-on view. (d) EM map of the ternary complex with the fitted ubiquitin orientations from (b) and PCNA (PDB ID 1VYM) (e) EM map of the ternary complex with the fitted split-fusion PCNA crystal structure.