2MF0

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


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 2500 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of the non-coding RNA RsmZ acting as a protein sponge.

Duss, O.Michel, E.Yulikov, M.Schubert, M.Jeschke, G.Allain, F.H.

(2014) Nature 509: 588-592

  • DOI: 10.1038/nature13271
  • Primary Citation of Related Structures:  

  • PubMed 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 v ...

    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'.


    Organizational Affiliation

    Institute of Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbon storage regulator homolog
A, B, C, D, E, F
70Pseudomonas protegens (strain DSM 19095 / LMG 27888 / CHA0)Mutation(s): 0 
Gene Names: csrA1 (rsmE)
Find proteins for P0DPC3 (Pseudomonas protegens (strain DSM 19095 / LMG 27888 / CHA0))
Go to UniProtKB:  P0DPC3
Entity ID: 2
MoleculeChainsLengthOrganism
RNA_(72-MER)G72N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 2500 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2014-07-02
    Type: Database references