4JRK

Crystal Structure of Escherichia coli Hfq Surface Mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.894 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mapping Hfq-RNA interaction surfaces using tryptophan fluorescence quenching.

Robinson, K.E.Orans, J.Kovach, A.R.Link, T.M.Brennan, R.G.

(2014) Nucleic Acids Res. 42: 2736-2749

  • DOI: 10.1093/nar/gkt1171
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Hfq is a posttranscriptional riboregulator and RNA chaperone that binds small RNAs and target mRNAs to effect their annealing and message-specific regulation in response to environmental stressors. Structures of Hfq-RNA complexes indicate that U-rich ...

    Hfq is a posttranscriptional riboregulator and RNA chaperone that binds small RNAs and target mRNAs to effect their annealing and message-specific regulation in response to environmental stressors. Structures of Hfq-RNA complexes indicate that U-rich sequences prefer the proximal face and A-rich sequences the distal face; however, the Hfq-binding sites of most RNAs are unknown. Here, we present an Hfq-RNA mapping approach that uses single tryptophan-substituted Hfq proteins, all of which retain the wild-type Hfq structure, and tryptophan fluorescence quenching (TFQ) by proximal RNA binding. TFQ properly identified the respective distal and proximal binding of A15 and U6 RNA to Gram-negative Escherichia coli (Ec) Hfq and the distal face binding of (AA)3A, (AU)3A and (AC)3A to Gram-positive Staphylococcus aureus (Sa) Hfq. The inability of (GU)3G to bind the distal face of Sa Hfq reveals the (R-L)n binding motif is a more restrictive (A-L)n binding motif. Remarkably Hfq from Gram-positive Listeria monocytogenes (Lm) binds (GU)3G on its proximal face. TFQ experiments also revealed the Ec Hfq (A-R-N)n distal face-binding motif should be redefined as an (A-A-N)n binding motif. TFQ data also demonstrated that the 5'-untranslated region of hfq mRNA binds both the proximal and distal faces of Ec Hfq and the unstructured C-terminus.


    Organizational Affiliation

    Department of Biochemistry, Duke University, Durham, NC 27710, USA and Department of Biochemistry and Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein hfq
A, B, C
68Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: hfq
Find proteins for P0A6X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6X3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.894 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.177 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 33.410α = 90.00
b = 66.309β = 90.00
c = 85.106γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PHENIXrefinement
HKL-3000data scaling
CCP4phasing
CCP4model building
HKL-3000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2014-03-12
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description