Structural insights into ATP hydrolysis by the MoxR ATPase RavA and the LdcI-RavA cage-like complex

摘要

Pseudo-atomic model of the LdcI–RavA complex, based on flexible fitting of crystal structures of RavA (PDB ID: 3NBX) and LdcI (PDB ID: 3N75) . The cryo-EM map used for fitting corresponds to the “Class 1” map after 3D classification (containing two LdcI decamers and one RavA hexamer, see panel ) to which C5 symmetry has been applied. Two LdcI decamers (coloured yellow and orange) and five spiral RavA hexamers (individually coloured light to dark blue) are shown as cartoons. Top and side views are shown, as well as a cut-away side view displaying the inner cavity of the cage. A dashed box ( ) shows one RavA monomer with annotations for the different domains: AAA+ module (green), triple helical domain (red), and LARA domain (blue). The seam in the spiral RavA hexamer is indicated by a dashed line. , Classes 1 ( ) and 2 ( ) obtained after C5 symmetry expansion followed by a masked 3D classification without angular search in RELION-2.0, resulting in C1 asymmetric maps. For each class, a post-processed cryo-EM map is shown (left) along with a fit of two LdcI decamers (yellow and orange) and one RavA hexamer (Class 1: cyan, Class 2: dark blue). Dashed lines indicate the positions of the masked-out RavA hexamers during symmetry expansion. On the right, side and top views of the fits are shown, with panels ( )–( ) (dashed boxes) focusing on specific LARA domains (numbered 1–6, black circles: rigid, red circles: flexible) contacting LdcI and their corresponding fits in the EM map. Class 2 displays a 6° tilted orientation of the second LdcI decamer (coloured orange) compared to Class 1.