Figure 1. Cage-like architecture of the LdcI–RavA complex (11 Å resolution).
(A) Top view with LdcI facing the reader, (B) Side view with RavA facing the reader. For this RavA hexamer, LARA domain positions are indicated by ellipses (solid black for the two LARA domains interacting with the inner LdcI rings from above, dotted black for the two LARA domains interacting with the outer LdcI rings from underneath and invisible from this orientation, solid dark blue for the LARA domains interacting equatorially with the triple helical domains of adjacent RavA monomers). (C) Side cut-away view. Complex dimensions are indicated.
Figure 1—figure supplement 1. Structures of the individual RavA hexamer and the LdcI decamer.
(A) Pseudoatomic model of the RavA hexamer based on rigid fitting of the crystal structure of the RavA monomer into the negative stain EM map of the RavA-ADP hexamer (El Bakkouri et al., 2010). Each monomer is colored differently. One of the RavA protomers is colored to highlight its domain composition. (B) Crystal structure of the D5-symmetrical LdcI decamer (Kanjee et al., 2011). ppGpp is shown as black spheres.
Figure 1—figure supplement 2. CryoEM analysis of the LdcI–RavA cage.
(A) CryoEM micrograph of LdcI–RavA displaying particle boxing. (B) Correspondence between projections of the 3D model and particle class averages, illustrating the reliability of the 3D reconstruction. (C) Angular distribution for particles used for the final 3D reconstruction shown for the asymmetric unit. (D) Gold-standard FSC curves calculated for unmasked (blue) and soft shaped masked (red) maps, indicating the resolution of 14 Å and 11 Å respectively according to FSC = 0.143 criterion. (E) Comparison between the initial negative stain EM map (Snider et al., 2006), the cryoET sub-tomogram average map used as an initial model for refinement in this study and the final 11 Å cryoEM map.