Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C6  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 23.52 kDa 
• Atom Count: 1902 
• Modelled Residue Count: 197 
• Deposited Residue Count: 210 
• Unique protein chains: 1

3HFO

Crystal Structure of an Hfq protein from Synechocystis sp.

• PDB DOI: 10.2210/pdb3HFO/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Synechocystis sp. PCC 6803
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-12 Released: 2009-07-14 
• Deposition Author(s): Boggild, A., Overgaard, M., Valentin-Hansen, P., Brodersen, D.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.200 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 

Literature

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

• PubMed: 19777643 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ssr3341 protein	A, B, C	70	Synechocystis sp. PCC 6803	Mutation(s): 0  Gene Names: ssr3341
UniProt
Find proteins for P74112 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P74112  Go to UniProtKB:  P74112

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.200 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 
• Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.47	α = 90
b = 86.16	β = 90
c = 103.18	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-05-12 
• Released Date: 2009-07-14 
Deposition Author(s): Boggild, A., Overgaard, M., Valentin-Hansen, P., Brodersen, D.E.

Revision History  

• Version 1.0: 2009-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-11-16
  Changes: Atomic model
• Version 1.3: 2012-03-21
  Changes: Database references
• Version 1.4: 2018-03-07
  Changes: Data collection