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: 49.55 kDa 
• Atom Count: 3717 
• Modelled Residue Count: 400 
• Deposited Residue Count: 444 
• Unique protein chains: 1

2YLB

Structure of Salmonella typhimurium Hfq at 1.15 A

• PDB DOI: 10.2210/pdb2YLB/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-06-01 Released: 2011-07-20 
• Deposition Author(s): Sauer, E., Weichenrieder, O.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.208 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Literature

Structural Basis for RNA 3' End Recognition by Hfq

Sauer, E., Weichenrieder, O.

(2011) Proc Natl Acad Sci U S A 108: 13065

• PubMed: 21737752 
• DOI: 10.1073/pnas.1103420108
• Primary Citation of Related Structures:  
  2YLB, 2YLC


• PubMed Abstract: 
  

The homohexameric (L)Sm protein Hfq is a central mediator of small RNA-based gene regulation in bacteria. Hfq recognizes small regulatory RNAs (sRNAs) specifically, despite their structural diversity. This specificity could not be explained by previously described RNA-binding modes of Hfq. Here we present a distinct and preferred mode of Hfq-RNA interaction that involves the direct recognition of a uridine-rich RNA 3' end. This feature is common in bacterial RNA transcripts as a consequence of Rho-independent transcription termination and hence likely contributes significantly to the general recognition of sRNAs by Hfq. Isothermal titration calorimetry shows nanomolar affinity between Salmonella typhimurium Hfq and a hexauridine substrate. We determined a crystal structure of the complex that reveals a constricted RNA backbone conformation in the proximal RNA-binding site of Hfq, allowing for a direct protein contact of the 3' hydroxyl group. A free 3' hydroxyl group is crucial for the high-affinity interaction with Hfq also in the context of a full-length sRNA substrate, RybB. The capacity of Hfq to occupy and sequester the RNA 3' end has important implications for the mechanisms by which Hfq is thought to affect sRNA stability, turnover, and regulation.

---

Organizational Affiliation: 

Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN HFQ	A, B, C, D, E, F	74	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: hfq, STM4361
UniProt
Find proteins for P0A1R0 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0A1R0  Go to UniProtKB:  P0A1R0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.208 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.4	α = 90
b = 61.4	β = 90
c = 167.03	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-06-01 
• Released Date: 2011-07-20 
Deposition Author(s): Sauer, E., Weichenrieder, O.

Revision History  

• Version 1.0: 2011-07-20
  Type: Initial release
  
• Version 1.1: 2011-08-03
  Changes: Atomic model, Other
• Version 1.2: 2011-08-24
  Changes: Database references