2MF1: Structural basis of the non-coding RNA RsmZ acting as protein sponge: Conformer R of RsmZ(1-72)/RsmE(dimer) 1to3 complex

Citation:
Abstract
MicroRNA and protein sequestration by non-coding RNAs (ncRNAs) has recently generated much interest. In the bacterial Csr/Rsm system, which is considered to be the most general global post-transcriptional regulatory system responsible for bacterial virulence, ncRNAs such as CsrB or RsmZ activate translation initiation by sequestering homodimeric CsrA-type proteins from the ribosome-binding site of a subset of messenger RNAs. However, the mechanism of ncRNA-mediated protein sequestration is not understood at the molecular level. Here we show for Pseudomonas fluorescens that RsmE protein dimers assemble sequentially, specifically and cooperatively onto the ncRNA RsmZ within a narrow affinity range. This assembly yields two different native ribonucleoprotein structures. Using a powerful combination of nuclear magnetic resonance and electron paramagnetic resonance spectroscopy we elucidate these 70-kilodalton solution structures, thereby revealing the molecular mechanism of the sequestration process and how RsmE binding protects the ncRNA from RNase E degradation. Overall, our findings suggest that RsmZ is well-tuned to sequester, store and release RsmE and therefore can be viewed as an ideal protein 'sponge'.
PDB ID: 2MF1Download
MMDB ID: 119986
PDB Deposition Date: 2013/10/2
Updated in MMDB: 2014/07
Experimental Method:
solution nmr
Source Organism:
Pseudomonas protegens Pf-5
Similar Structures:
Biological Unit for 2MF1: heptameric; determined by author
Molecular Components in 2MF1
Label Count Molecule
Proteins (6 molecules)
6
Carbon Storage Regulator Homolog
Molecule annotation
Nucleotide(1 molecule)
1
RNA_(72-mer)
Molecule annotation
* Click molecule labels to explore molecular sequence information.

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