2MFG: Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(SL4)/RsmE(dimer) 2:1 complex

The carbon storage regulator/regulator of secondary metabolism (Csr/Rsm) type of small non-coding RNAs (sRNAs) is widespread throughout bacteria and acts by sequestering the global translation repressor protein CsrA/RsmE from the ribosome binding site of a subset of mRNAs. Although we have previously described the molecular basis of a high affinity RNA target bound to RsmE, it remains unknown how other lower affinity targets are recognized by the same protein. Here, we have determined the nuclear magnetic resonance solution structures of five separate GGA binding motifs of the sRNA RsmZ of Pseudomonas fluorescens in complex with RsmE. The structures explain how the variation of sequence and structural context of the GGA binding motifs modulate the binding affinity for RsmE by five orders of magnitude ( approximately 10 nM to approximately 3 mM, Kd). Furthermore, we see that conformational adaptation of protein side-chains and RNA enable recognition of different RNA sequences by the same protein contributing to binding affinity without conferring specificity. Overall, our findings illustrate how the variability in the Csr/Rsm protein-RNA recognition allows a fine-tuning of the competition between mRNAs and sRNAs for the CsrA/RsmE protein.
PDB ID: 2MFGDownload
MMDB ID: 117766
PDB Deposition Date: 2013/10/11
Updated in MMDB: 2018/05
Experimental Method:
solution nmr
Source Organism:
Pseudomonas fluorescens
Similar Structures:
Biological Unit for 2MFG: tetrameric; determined by author
Molecular Components in 2MFG
Label Count Molecule
Proteins (2 molecules)
Carbon Storage Regulator Homolog
Molecule annotation
Nucleotide(1 molecule)
Sl4(rsmz) RNA
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB