Biological Assembly 1  

 3D View: Structure | Electron Density

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: 49.55 kDa 
• Atom Count: 3240 
• Residue Count: 394 
• Unique protein chains: 1

1HK9

Crystal structure of the Hfq protein from Escherichia coli

• DOI: 10.2210/pdb1HK9/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2003-03-06 Released: 2003-07-24 
• Deposition Author(s): Sauter, C., Basquin, J., Suck, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.262 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Literature

Sm-Like Proteins in Eubacteria: The Crystal Structure of the Hfq Protein from Escherichia Coli

Sauter, C., Basquin, J., Suck, D.

(2003) Nucleic Acids Res 31: 4091

• PubMed: 12853626 
• DOI: 10.1093/nar/gkg480
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The Hfq protein was discovered in Escherichia coli in the early seventies as a host factor for the Qbeta phage RNA replication. During the last decade, it was shown to be involved in many RNA processing events and remote sequence homology indicated a link to spliceosomal Sm proteins. We report the crystal structure of the E.coli Hfq protein showing that its monomer displays a characteristic Sm-fold and forms a homo-hexamer, in agreement with former biochemical data. Overall, the structure of the E.coli Hfq ring is similar to the one recently described for Staphylococcus aureus. This confirms that bacteria contain a hexameric Sm-like protein which is likely to be an ancient and less specialized form characterized by a relaxed RNA binding specificity. In addition, we identified an Hfq ortholog in the archaeon Methanococcus jannaschii which lacks a classical Sm/Lsm gene. Finally, a detailed structural comparison shows that the Sm-fold is remarkably well conserved in bacteria, Archaea and Eukarya, and represents a universal and modular building unit for oligomeric RNA binding proteins.

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Related Citations: 

• The Sm-Like Hfq Protein Increases Oxys RNA Interaction with Target Mrnas
  Zhang, A., Wassarman, K.M., Ortega, J., Steven, A.C., Storz, G.
  (2002) Mol Cell 9: 11

• Hfq: A Bacterial Sm-Like Protein that Mediates RNA-RNA Interaction
  Moller, T., Franch, T., Hojrup, P., Keene, D.R., Bachinger, H.P., Brennan, R.G., Valentin-Hansen, P.
  (2002) Mol Cell 9: 23

• Structures of the Pleiotropic Translational Regulator Hfq and an Hfq-RNA Complex: A Bacterial Sm-Like Protein
  Schumacher, M.A., Pearson, R.F., Moller, T., Valentin-Hansen, P., Brennan, R.G.
  (2002) EMBO J 21: 3546

• Characterization of Broadly Pleiotropic Phenotypes Caused by an Hfq Insertion Mutation in Escherichia Coli K-12
  Tsui, H.C., Leung, H.C., Winkler, M.E.
  (1994) Mol Microbiol 13: 35

• Bacterial Proteins Required for Replication of Phage Q Ribonucleic Acid. Purification and Properties of Host Factor I, a Ribonucleic Acid-Binding Protein
  De Fernandez, M.T.F., Hayward, W.S., August, J.T.
  (1972) J Biol Chem 247: 824

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Organizational Affiliation: 

European Molecular Biology Laboratory, Structural and Computational Biology Programme, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN HFQ	A, B, C, D, E, F	74	Escherichia coli	Mutation(s): 0
Find proteins for P0A6X3 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A6X3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.262 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.35	α = 90
b = 61.35	β = 90
c = 166.1	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-03-06 
• Released Date: 2003-07-24 
Deposition Author(s): Sauter, C., Basquin, J., Suck, D.

Revision History 

• Version 1.0: 2003-07-24
  Type: Initial release
  
• Version 1.1: 2011-07-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2019-05-15
  Changes: Data collection, Experimental preparation