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Figure 5.
Figure 5. Global view of the nucleolin RBD12/b2NRE complex
structure. The lowest-energy structure is shown. a, Stereoview
of the complex, showing b2NRE and nucleolin RBD12 in stick and
ribbon representations, respectively. The b2NRE (orange) loop is
sandwiched between the two RBDs, with RBD1 (blue) interacting
with nucleotides at the 3' side of the RNA (C12, G13 and A14)
and RBD2 (green) contacting nucleotides of the 5' side (U9 and
C10). The linker (red) spans the major groove of the loop. Some
of the amino acid side-chains (green) at the interface (Y58,
F56, K94, R127, Y140) are shown in stick representation. b,
Surface representation of the whole complex. The side-chains of
linker residues K95 and R97 (red), pack closely against the RNA.
The view and color scheme is the same as in a. c, Surface
representation of the whole complex with the molecule turned
 vert,
similar 180° relative to b, showing the two holes in the RNA
loop. The linker residue K94 (red) inserts into the upper hole,
whereas R97 packs against the lower hole, possibly involved in
water-mediated interactions with the RNA.
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