Crystal Structure of an Hfq protein from Anabaena sp.

Experimental Data Snapshot

  • Resolution: 2.31 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.272 
  • R-Value Observed: 0.273 

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This is version 1.3 of the entry. See complete history


Cyanobacteria contain a structural homologue of the Hfq protein with altered RNA-binding properties.

Boggild, A.Overgaard, M.Valentin-Hansen, P.Brodersen, D.E.

(2009) FEBS J 276: 3904-3915

  • DOI: https://doi.org/10.1111/j.1742-4658.2009.07104.x
  • Primary Citation of Related Structures:  
    3HFN, 3HFO

  • PubMed Abstract: 

    Hfq proteins are common in many species of enterobacteria, where they participate in RNA folding and translational regulation through pairing of small RNAs and messenger RNAs. Hfq proteins share the distinctive Sm fold, and form ring-shaped structures similar to those of the Sm/Lsm proteins regulating mRNA turnover in eukaryotes. However, bacterial Hfq proteins are homohexameric, whereas eukaryotic Sm/Lsm proteins are heteroheptameric. Recently, Hfq proteins with poor sequence conservation were identified in archaea and cyanobacteria. In this article, we describe crystal structures of the Hfq proteins from the cyanobacteria Synechocystis sp. PCC 6803 and Anabaena PCC 7120 at 1.3 and 2.3 A resolution, respectively, and show that they retain the classic Sm fold despite low sequence conservation. In addition, the intersubunit contacts and RNA-binding site are divergent, and we show biochemically that the proteins bind very weakly to known Escherichia coli Hfq target RNAs in vitro. Moreover, when expressed in E. coli, the proteins cannot mediate Hfq-dependent RNA regulation. It therefore appears that the cyanobacterial proteins constitute a specialized subfamily of Hfq proteins that bind relatively weakly to A/U-rich tracks of regulatory RNAs. The results have implications for our understanding of the evolution of the Sm fold and the Hfq proteins in the bacterial kingdom in general.

  • Organizational Affiliation

    Centre for mRNP Biogenesis and Metabolism, University of Aarhus, Denmark,

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Asl2047 protein
A, B
72Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: asl2047
Find proteins for Q8YVD1 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore Q8YVD1 
Go to UniProtKB:  Q8YVD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8YVD1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.31 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.272 
  • R-Value Observed: 0.273 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.58α = 90
b = 60.58β = 90
c = 32.47γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2012-03-21
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description