4PNO

Escherichia coli Hfq-RNA complex at 0.97 A Resolution

• PDB DOI: https://doi.org/10.2210/pdb4PNO/pdb

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


• Deposited: 2014-05-24 Released: 2014-11-19 
• Deposition Author(s): Schulz, E.C., Barabas, O.
• Funding Organization(s): EU FP7 - Marie Curie IEF

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.97 Å
• R-Value Free: 0.164 
• R-Value Work: 0.142 
• R-Value Observed: 0.144 

Starting Model: experimental

Literature

Structure of an Escherichia coli Hfq:RNA complex at 0.97 angstrom resolution.

Schulz, E.C., Barabas, O.

(2014) Acta Crystallogr F Struct Biol Commun 70: 1492-1497

• PubMed: 25372815 
• DOI: https://doi.org/10.1107/S2053230X14020044
• Primary Citation of Related Structures:  
  4PNO


• PubMed Abstract: 
  

  In bacteria, small RNAs (sRNAs) silence or activate target genes through base pairing with the mRNA, thereby modulating its translation. A central player in this process is the RNA chaperone Hfq, which facilitates the annealing of sRNAs with their target mRNAs. Hfq has two RNA-binding surfaces that recognize A-rich and U-rich sequences, and is believed to bind an sRNA-mRNA pair simultaneously. However, how Hfq promotes annealing remains unclear. Here, the crystal structure of Escherichia coli Hfq is presented in complex with U6-RNA bound to its proximal binding site at 0.97 Å resolution, revealing the Hfq-RNA interaction in exceptional detail.

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Organizational Affiliation: 

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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: 8.45 kDa 
• Atom Count: 653 
• Modelled Residue Count: 64 
• Deposited Residue Count: 72 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-binding protein Hfq	A	72	Escherichia coli	Mutation(s): 0  Gene Names: hfq, BN17_41491, BU34_16545, ECs5148, LF82_0993
UniProt
Find proteins for C1IFD2 (Escherichia coli) Explore C1IFD2  Go to UniProtKB:  C1IFD2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U5P	B [auth A]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.97 Å
• R-Value Free: 0.164 
• R-Value Work: 0.142 
• R-Value Observed: 0.144 
• Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.11	α = 90
b = 61.11	β = 90
c = 27.86	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-11-19 
Deposition Author(s): Schulz, E.C., Barabas, O.

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Funding Organization	Location	Grant Number
EU FP7 - Marie Curie IEF	Germany	PIEF-GA-2011-301489

Revision History  

• Version 1.0: 2014-11-19
  Type: Initial release
  
• Version 1.1: 2014-11-26
  Changes: Data collection
• Version 1.2: 2018-03-07
  Changes: Advisory, Data collection, Derived calculations, Other, Source and taxonomy
• Version 1.3: 2023-09-27
  Changes: Advisory, Data collection, Database references, Refinement description