5NEW

RNA-RNA base stacking in the crystal structure of an Hfq6:RNA dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.511 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq.

Schulz, E.C.Seiler, M.Zuliani, C.Voigt, F.Rybin, V.Pogenberg, V.Mucke, N.Wilmanns, M.Gibson, T.J.Barabas, O.

(2017) Sci Rep 7: 9903-9903

  • DOI: 10.1038/s41598-017-10085-8

  • PubMed Abstract: 
  • The RNA-chaperone Hfq catalyses the annealing of bacterial small RNAs (sRNAs) with target mRNAs to regulate gene expression in response to environmental stimuli. Hfq acts on a diverse set of sRNA-mRNA pairs using a variety of different molecular mech ...

    The RNA-chaperone Hfq catalyses the annealing of bacterial small RNAs (sRNAs) with target mRNAs to regulate gene expression in response to environmental stimuli. Hfq acts on a diverse set of sRNA-mRNA pairs using a variety of different molecular mechanisms. Here, we present an unusual crystal structure showing two Hfq-RNA complexes interacting via their bound RNA molecules. The structure contains two Hfq6:A18 RNA assemblies positioned face-to-face, with the RNA molecules turned towards each other and connected via interdigitating base stacking interactions at the center. Biochemical data further confirm the observed interaction, and indicate that RNA-mediated contacts occur between Hfq-RNA complexes with various (ARN)X motif containing RNA sequences in vitro, including the stress response regulator OxyS and its target, fhlA. A systematic computational survey also shows that phylogenetically conserved (ARN)X motifs are present in a subset of sRNAs, some of which share similar modular architectures. We hypothesise that Hfq can co-opt RNA-RNA base stacking, an unanticipated structural trick, to promote the interaction of (ARN)X motif containing sRNAs with target mRNAs on a "speed-dating" fashion, thereby supporting their regulatory function.


    Organizational Affiliation

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-binding protein Hfq
A, B
102Escherichia coli O45:K1 (strain S88 / ExPEC)Gene Names: hfq
Find proteins for B7MKX6 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MKX6
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')H6Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*U)-3')C2Escherichia coli
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.511 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.196 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 66.880α = 90.00
b = 66.880β = 90.00
c = 227.720γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-04
    Type: Initial release