SASDAG5: RNA shaperone Hfq (RNA chaperone Hfq, Hfq)

Basic information

• Entry: Database: SASBDB / ID: SASDAG5

Sample

RNA shaperone Hfq

• RNA chaperone Hfq (protein), Hfq, Escherichia coli

• Biological species: Escherichia coli (E. coli)
• Citation: Journal: Nucleic Acids Res / Year: 2011; Title: Structural insights into the dynamics and function of the C-terminus of the E. coli RNA chaperone Hfq.; Authors: Mads Beich-Frandsen / Branislav Vecerek / Petr V Konarev / Björn Sjöblom / Karin Kloiber / Hermann Hämmerle / Lukas Rajkowitsch / Andrew J Miles / Georg Kontaxis / B A Wallace / Dimitri I Svergun / Robert Konrat / Udo Bläsi / Kristina Djinovic-Carugo / ; Abstract: The hexameric Escherichia coli RNA chaperone Hfq (Hfq(Ec)) is involved in riboregulation of target mRNAs by small trans-encoded RNAs. Hfq proteins of different bacteria comprise an evolutionarily conserved core, whereas the C-terminus is variable in length. Although the structure of the conserved core has been elucidated for several Hfq proteins, no structural information has yet been obtained for the C-terminus. Using bioinformatics, nuclear magnetic resonance spectroscopy, synchrotron radiation circular dichroism (SRCD) spectroscopy and small angle X-ray scattering we provide for the first time insights into the conformation and dynamic properties of the C-terminal extension of Hfq(Ec). These studies indicate that the C-termini are flexible and extend laterally away from the hexameric core, displaying in this way features typical of intrinsically disordered proteins that facilitate intermolecular interactions. We identified a minimal, intrinsically disordered region of the C-terminus supporting the interactions with longer RNA fragments. This minimal region together with rest of the C-terminal extension provides a flexible moiety capable of tethering long and structurally diverse RNA molecules. Furthermore, SRCD spectroscopy supported the hypothesis that RNA fragments exceeding a certain length interact with the C-termini of Hfq(Ec).

Contact author

• Petr Konarev (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

Models

• Model #115: ; Type: dummy / Software: Dammin / Radius of dummy atoms: 1.90 A / Symmetry: P6 / Chi-square value: 6.853924; Search similar-shape structures of this assembly by Omokage search (details)
• Model #116: ; Type: mix / Software: Bunch / Radius of dummy atoms: 1.90 A / Symmetry: P6 / Chi-square value: 4.9284; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: RNA shaperone Hfq / Sample MW: 67.2 kDa / Specimen concentration: 2.30-18.50
• Buffer: Name: 50 mM Tris-HCL / pH: 7.5 / Composition: 150 mM NaCl, 1.0 mM DTT

Entity #90

Name: Hfq / Type: protein / Description: RNA chaperone Hfq / Formula weight: 11.2 / Num. of mol.: 6 / Source: Escherichia coli
Sequence:

MAKGQSLQDP FLNALRRERV PVSIYLVNGI KLQGQIESFD QFVILLKNTV SQMVYKHAIS TVVPSRPVSH HSNNAGGGTS SNYHHGSSAQ NTSAQQDSEE TE

Experimental information

• Beam: Instrument name: DORIS III X33 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron
• Detector: Name: MAR 345 Image Plate

Scan

Measurement date: May 2, 2008 / Storage temperature: 37 °C / Cell temperature: 37 °C / Exposure time: 120 sec. / Number of frames: 2 / Unit: 1/nm /

	Min	Max
Q	0.1549	5.1708

Distance distribution function P(R)

Sofotware P(R): GNOM 4.6 / Number of points: 416 /

	Min	Max
Q	0.1563	5.163
P(R) point	1	416
R	0	11

Result

D max: 11.2 / Type of curve: merged /

	Experimental	Porod
MW	67.2 kDa	-
Volume	-	110 nm3

	P(R)	Guinier
Forward scattering, I0	133	130
Radius of gyration, Rg	3.23 nm	3.2 nm