4V2S

Crystal structure of Hfq in complex with the sRNA RydC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.48 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Recognition of the small regulatory RNA RydC by the bacterial Hfq protein.

Dimastrogiovanni, D.Frohlich, K.S.Bandyra, K.J.Bruce, H.A.Hohensee, S.Vogel, J.Luisi, B.F.

(2014) Elife 3: --

  • DOI: 10.7554/eLife.05375

  • PubMed Abstract: 
  • Bacterial small RNAs (sRNAs) are key elements of regulatory networks that modulate gene expression. The sRNA RydC of Salmonella sp. and Escherichia coli is an example of this class of riboregulators. Like many other sRNAs, RydC bears a 'seed' region ...

    Bacterial small RNAs (sRNAs) are key elements of regulatory networks that modulate gene expression. The sRNA RydC of Salmonella sp. and Escherichia coli is an example of this class of riboregulators. Like many other sRNAs, RydC bears a 'seed' region that recognises specific transcripts through base-pairing, and its activities are facilitated by the RNA chaperone Hfq. The crystal structure of RydC in complex with E. coli Hfq at a 3.48 Å resolution illuminates how the protein interacts with and presents the sRNA for target recognition. Consolidating the protein-RNA complex is a host of distributed interactions mediated by the natively unstructured termini of Hfq. Based on the structure and other data, we propose a model for a dynamic effector complex comprising Hfq, small RNA, and the cognate mRNA target.


    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-BINDING PROTEIN HFQ
A, B, C, D, E, F
102Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: hfq
Find proteins for P0A6X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6X3
Entity ID: 2
MoleculeChainsLengthOrganism
RYDCQ65Salmonella enterica subsp. enterica serovar Typhimurium
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.48 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.940α = 90.00
b = 73.356β = 90.00
c = 137.947γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2019-02-27
    Type: Data collection, Database references, Other