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. Author manuscript; available in PMC: 2015 Feb 1.
Published in final edited form as: Nat Struct Mol Biol. 2014 Jul 13;21(8):679–685. doi: 10.1038/nsmb.2857

Figure 5. Two separate RNA binding sites in the ROQ domain.

Figure 5

(a). Overlay of the structures of the Hmg19 complex (in color) and TNF23 complex (gray) of the ROQ domain, based on domains II and III. A 30° change in the orientation of domain I is indicated with the red arrow. (b). EMSA results showing the formation of the ROQ-TNFds-Hmg19 ternary complex. Wild-type ROQ domain was pre-incubated with labeled TNFds, and then with increasing concentrations of unlabeled Hmg19. The NaCl concentration was 50 mM. (c). EMSA results with mutations in the A site. The mutations blocked the formation of the ternary complex. (d). A model showing possible linkages between the RNA molecules in the B site and A site. A single-stranded RNA (gray, 7 nts) was modeled to connect the 3′ end of the RNA in the B site to the 5′ end of the stem-loop RNA in the A site (~30 Å distance). A linker between the 3′ end of the RNA in the A site to the 5′ end of the RNA in the B site would need to span ~60 Å (gray dots).