4V2S

Crystal structure of Hfq in complex with the sRNA RydC

• PDB DOI: https://doi.org/10.2210/pdb4V2S/pdb
• NAKB: 4V2S

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Escherichia coli K-12, Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-14 Released: 2015-01-14 
• Deposition Author(s): Dimastrogiovanni, D., Frohlich, K.S., Bruce, H.A., Bandyra, K.J., Hohensee, S., Vogel, J., Luisi, B.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.48 Å
• R-Value Free: 0.282 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 

Starting Model: experimental

Literature

Recognition of the small regulatory RNA RydC by the bacterial Hfq protein.

Dimastrogiovanni, D., Frohlich, K.S., Bandyra, K.J., Bruce, H.A., Hohensee, S., Vogel, J., Luisi, B.F.

(2014) Elife 3

• PubMed: 25551292 
• DOI: https://doi.org/10.7554/eLife.05375
• Primary Citation of Related Structures:  
  4V2S


• PubMed Abstract: 
  

  Bacterial small RNAs (sRNAs) are key elements of regulatory networks that modulate gene expression. The sRNA RydC of Salmonella sp. and Escherichia coli is an example of this class of riboregulators. Like many other sRNAs, RydC bears a 'seed' region that recognises specific transcripts through base-pairing, and its activities are facilitated by the RNA chaperone Hfq. The crystal structure of RydC in complex with E. coli Hfq at a 3.48 Å resolution illuminates how the protein interacts with and presents the sRNA for target recognition. Consolidating the protein-RNA complex is a host of distributed interactions mediated by the natively unstructured termini of Hfq. Based on the structure and other data, we propose a model for a dynamic effector complex comprising Hfq, small RNA, and the cognate mRNA target.

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Organizational Affiliation: 

Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 87.78 kDa 
• Atom Count: 4,470 
• Modelled Residue Count: 475 
• Deposited Residue Count: 677 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-BINDING PROTEIN HFQ	A, B, C, D, E, F	102	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A6X3 (Escherichia coli (strain K12)) Explore P0A6X3  Go to UniProtKB:  P0A6X3

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RYDC	G [auth Q]	65	Salmonella enterica subsp. enterica serovar Typhimurium

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.48 Å
• R-Value Free: 0.282 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.94	α = 90
b = 73.356	β = 90
c = 137.947	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): Dimastrogiovanni, D., Frohlich, K.S., Bruce, H.A., Bandyra, K.J., Hohensee, S., Vogel, J., Luisi, B.F.

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 1.1: 2019-02-27
  Changes: Data collection, Database references, Other
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Other, Refinement description