3HSB

Crystal structure of YmaH (Hfq) from Bacillus subtilis in complex with an RNA aptamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq

Someya, T.Baba, S.Fujimoto, M.Kawai, G.Kumasaka, T.Nakamura, K.

(2012) Nucleic Acids Res. 40: 1856-1867

  • DOI: 10.1093/nar/gkr892

  • PubMed Abstract: 
  • Bacterial Hfq is a protein that plays an important role in the regulation of genes in cooperation with sRNAs. Escherichia coli Hfq (EcHfq) has two or more sites that bind RNA(s) including U-rich and/or the poly(A) tail of mRNA. However, functional an ...

    Bacterial Hfq is a protein that plays an important role in the regulation of genes in cooperation with sRNAs. Escherichia coli Hfq (EcHfq) has two or more sites that bind RNA(s) including U-rich and/or the poly(A) tail of mRNA. However, functional and structural information about Bacillus subtilis Hfq (BsHfq) including the RNA sequences that specifically bind to it remain unknown. Here, we describe RNA aptamers including fragment (AG)(3)A that are recognized by BsHfq and crystal structures of the BsHfq-(AG)(3)A complex at 2.2 Å resolution. Mutational and structural studies revealed that the RNA fragment binds to the distal site, one of the two binding sites on Hfq, and identified amino acid residues that are critical for sequence-specific interactions between BsHfq and (AG)(3)A. In particular, R32 appears to interact with G bases in (AG)(3)A. Poly(A) also binds to the distal site of EcHfq, but the overall RNA structure and protein-RNA interaction patterns engaged in the R32 residues of BsHfq-(AG)(3)A differ from those of EcHfq-poly(A). These findings provide novel insight into how the Hfq homologue recognizes RNA.


    Related Citations: 
    • Expression, crystallization and preliminary crystallographic analysis of YmaH (Hfq) from Bacillus subtilis in complex with an RNA aptamer.
      Baba, S.,Someya, T.,Kumasaka, T.,Kawai, G.,Nakamura, K.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba-shi, Ibaraki 305-8572, Japan. tsomeya@biol.tsukuba.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein hfq
A, B, C, D, E, F
78Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: hfq (ymaH)
Find proteins for O31796 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O31796
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*GP*AP*GP*AP*GP*A)-3')X7N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.214 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 123.700α = 90.00
b = 123.700β = 90.00
c = 119.131γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
BSSdata collection
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-10-03
    Type: Database references