1rkj

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Solution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target

Overview

Nucleolin is a 70 kDa multidomain protein involved in several steps of, eukaryotic ribosome biogenesis. In vitro selection in combination with, mutagenesis and structural analysis identified binding sites in pre-rRNA, with the consensus (U/G)CCCG(A/G) in the context of a hairpin structure, the nucleolin recognition element (NRE). The central region of the protein, contains four tandem RNA-binding domains (RBDs), of which the first two, are responsible for the RNA-binding specificity and affinity for NREs., Here, we present the solution structure of the 28 kDa complex formed by, the two N-terminal RNA-binding domains of nucleolin (RBD12) and a natural, pre-rRNA target, b2NRE. The structure demonstrates that the, sequence-specific recognition of the pre-rRNA NRE is achieved by, intermolecular hydrogen bonds and stacking interactions involving mainly, the beta-sheet surfaces of the two RBDs and the linker residues. A, comparison with our previously determined NMR structure of RBD12 in, complex with an in vitro selected RNA target, sNRE, shows that although, the sequence-specific recognition of the loop consensus nucleotides is the, same in the two complexes, they differ in several aspects. While the, protein makes numerous specific contacts to the non-consensus nucleotides, in the loop E motif (S-turn) in the upper part of the sNRE stem, nucleolin, RBD12 contacts only consensus nucleotides in b2NRE. The absence of these, upper stem contacts from the RBD12/b2NRE complex results in a much less, stable complex, as demonstrated by kinetic analyses. The role of the loop, E motif in high-affinity binding is supported by gel-shift analyses with a, series of sNRE mutants. The less stable interaction of RBD12 with the, natural RNA target is consistent with the proposed role of nucleolin as a, chaperone that interacts transiently with pre-rRNA to prevent misfolding.

About this Structure

1RKJ is a Single protein structure of sequence from Mesocricetus auratus. Full crystallographic information is available from OCA.

Reference

Solution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target., Johansson C, Finger LD, Trantirek L, Mueller TD, Kim S, Laird-Offringa IA, Feigon J, J Mol Biol. 2004 Apr 2;337(4):799-816. PMID:15033352

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