3GIB

Crystal Structure of the Complex of the E. coli Hfq with Poly(A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of Escherichia coli Hfq bound to polyriboadenylate RNA

Link, T.M.Valentin-Hansen, P.Brennan, R.G.

(2009) Proc.Natl.Acad.Sci.USA 106: 19292-19297

  • DOI: 10.1073/pnas.0908744106

  • PubMed Abstract: 
  • Hfq is a small, highly abundant hexameric protein that is found in many bacteria and plays a critical role in mRNA expression and RNA stability. As an "RNA chaperone," Hfq binds AU-rich sequences and facilitates the trans annealing of small RNAs (sRN ...

    Hfq is a small, highly abundant hexameric protein that is found in many bacteria and plays a critical role in mRNA expression and RNA stability. As an "RNA chaperone," Hfq binds AU-rich sequences and facilitates the trans annealing of small RNAs (sRNAs) to their target mRNAs, typically resulting in the down-regulation of gene expression. Hfq also plays a key role in bacterial RNA decay by binding tightly to polyadenylate [poly(A)] tracts. The structural mechanism by which Hfq recognizes and binds poly(A) is unknown. Here, we report the crystal structure of Escherichia coli Hfq bound to the poly(A) RNA, A(15). The structure reveals a unique RNA binding mechanism. Unlike uridine-containing sequences, which bind to the "proximal" face, the poly(A) tract binds to the "distal" face of Hfq using 6 tripartite binding motifs. Each motif consists of an adenosine specificity site (A site), which is effected by peptide backbone hydrogen bonds, a purine nucleotide selectivity site (R site), and a sequence-nondiscriminating RNA entrance/exit site (E site). The resulting implication that Hfq can bind poly(A-R-N) triplets, where R is a purine nucleotide and N is any nucleotide, was confirmed by binding studies. Indeed, Hfq bound to the oligoribonucleotides (AGG)(8), (AGC)(8), and the shorter (A-R-N)(4) sequence, AACAACAAGAAG, with nanomolar affinities. The abundance of (A-R-N)(4) and (A-R-N)(5) triplet repeats in the E. coli genome suggests additional RNA targets for Hfq. Further, the structure provides insight into Hfq-mediated sRNA-mRNA annealing and the role of Hfq in RNA decay.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Texas, MD Anderson Cancer Center, Houston, TX 77030-4009, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein hfq
A, B, C
68Escherichia 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
5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'H9N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NHE
Query on NHE

Download SDF File 
Download CCD File 
A, C
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
N-CYCLOHEXYLTAURINE; CHES
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.223 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 66.534α = 90.00
b = 88.960β = 90.00
c = 39.635γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-02-01
    Type: Structure summary
  • Version 1.3: 2018-04-04
    Type: Advisory, Data collection