5NEW

RNA-RNA base stacking in the crystal structure of an Hfq6:RNA dimer

Summary for 5NEW

• Entry DOI: 10.2210/pdb5new/pdb
• Descriptor: RNA-binding protein Hfq, RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3'), RNA (5'-R(P*UP*U)-3'), ... (5 entities in total)
• Functional Keywords: hfq srna rna-rna interaction base stacking, rna
• Biological source: Escherichia coli S88; More
• Total number of polymer chains: 4
• Total formula weight: 25336.67

Authors

Schulz, E.C.,Barabas, O. (deposition date: 2017-03-12, release date: 2017-10-04, Last modification date: 2024-05-08)

Primary citation

Schulz, E.C.,Seiler, M.,Zuliani, C.,Voigt, F.,Rybin, V.,Pogenberg, V.,Mucke, N.,Wilmanns, M.,Gibson, T.J.,Barabas, O.
Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq.
Sci Rep, 7:9903-9903, 2017

PubMed Abstract: The RNA-chaperone Hfq catalyses the annealing of bacterial small RNAs (sRNAs) with target mRNAs to regulate gene expression in response to environmental stimuli. Hfq acts on a diverse set of sRNA-mRNA pairs using a variety of different molecular mechanisms. Here, we present an unusual crystal structure showing two Hfq-RNA complexes interacting via their bound RNA molecules. The structure contains two Hfq:A RNA assemblies positioned face-to-face, with the RNA molecules turned towards each other and connected via interdigitating base stacking interactions at the center. Biochemical data further confirm the observed interaction, and indicate that RNA-mediated contacts occur between Hfq-RNA complexes with various (ARN) motif containing RNA sequences in vitro, including the stress response regulator OxyS and its target, fhlA. A systematic computational survey also shows that phylogenetically conserved (ARN) motifs are present in a subset of sRNAs, some of which share similar modular architectures. We hypothesise that Hfq can co-opt RNA-RNA base stacking, an unanticipated structural trick, to promote the interaction of (ARN) motif containing sRNAs with target mRNAs on a "speed-dating" fashion, thereby supporting their regulatory function.

PubMed: 28852099
DOI: 10.1038/s41598-017-10085-8

Experimental method

X-RAY DIFFRACTION (2.511 Å)