5WQ1

Solution Structure of the first stem-loop of Escherichia coli DsrA RNA

  • Classification: RNA
  • Organism(s): Escherichia coli

  • Deposited: 2016-11-22 Released: 2017-07-05 
  • Deposition Author(s): Wu, P., Wu, J., Shi, Y.
  • Funding Organization(s): Ministry of Science and Technology of China; Strategic Priority Research Program of the Chinese Academy of Sciences; Chinese National Natural Science Foundation 

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 160 
  • 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

The important conformational plasticity of DsrA sRNA for adapting multiple target regulation

Wu, P.Liu, X.Yang, L.Sun, Y.Gong, Q.Wu, J.Shi, Y.

(2017) Nucleic Acids Res. 45: 9625-9639

  • DOI: 10.1093/nar/gkx570

  • PubMed Abstract: 
  • In bacteria, small non-coding RNAs (sRNAs) could function in gene regulations under variable stress responses. DsrA is an ∼90-nucleotide Hfq-dependent sRNA found in Escherichia coli. It regulates the translation and degradation of multiple mRNAs, suc ...

    In bacteria, small non-coding RNAs (sRNAs) could function in gene regulations under variable stress responses. DsrA is an ∼90-nucleotide Hfq-dependent sRNA found in Escherichia coli. It regulates the translation and degradation of multiple mRNAs, such as rpoS, hns, mreB and rbsD mRNAs. However, its functional structure and particularly how it regulates multiple mRNAs remain obscure. Using NMR, we investigated the solution structures of the full-length and isolated stem-loops of DsrA. We first solved the NMR structure of the first stem-loop (SL1), and further studied the melting process of the SL1 induced by the base-pairing with the rpoS mRNA and the A-form duplex formation of the DsrA/rpoS complex. The secondary structure of the second stem-loop (SL2) was also determined, which contains a lower stem and an upper stem with distinctive stability. Interestingly, two conformational states of SL2 in dynamic equilibrium were observed in our NMR spectra, suggesting that the conformational selection may occur during the base-pairing between DsrA and mRNAs. In summary, our study suggests that the conformational plasticity of DsrA may represent a special mechanism sRNA employed to deal with its multiple regulatory targets of mRNA.


    Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui 230027, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DsrA-SL1A23Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 160 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-11-22 
  • Released Date: 2017-07-05 
  • Deposition Author(s): Wu, P., Wu, J., Shi, Y.

Funding OrganizationCountryGrant Number
Ministry of Science and Technology of ChinaChina2016YFA0500700
Strategic Priority Research Program of the Chinese Academy of SciencesChinaXDB08010100
Strategic Priority Research Program of the Chinese Academy of SciencesChinaXDB08030302
Chinese National Natural Science FoundationChina31330018

Revision History 

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2017-11-01
    Type: Database references