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 
  • R-Value Observed: 0.220 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.7554/eLife.05375
  • Primary Citation of Related Structures:  
    4V2S

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-BINDING PROTEIN HFQ
A, B, C, D, E
A, B, C, D, E, F
102Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A6X3 (Escherichia coli (strain K12))
Explore P0A6X3 
Go to UniProtKB:  P0A6X3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6X3
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
RYDCG [auth Q]65Salmonella enterica subsp. enterica serovar Typhimurium
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.48 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.94α = 90
b = 73.356β = 90
c = 137.947γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2019-02-27
    Changes: Data collection, Database references, Other
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Other, Refinement description