2MFH

Csr/Rsm protein-RNA recognition - A molecular affinity ruler: RsmZ(36-44)/RsmE(dimer) 2:1 complex


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 999 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition.

Duss, O.Michel, E.Diarra Dit Konte, N.Schubert, M.Allain, F.H.

(2014) Nucleic Acids Res. 42: 5332-5346

  • DOI: 10.1093/nar/gku141
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 sit ...

    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 (∼10 nM to ∼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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbon storage regulator homolog
A, C
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
RsmZ(36-44) RNAB,D9N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 999 
  • 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: 2014-02-26
    Type: Initial release
  • Version 1.1: 2014-03-26
    Type: Database references
  • Version 1.2: 2014-05-14
    Type: Database references