SASDAH5: Complex of Hfq with DsrA (RNA chaperone Hfq, Hfq + RNA DsrA, Hfq_DsrA)

Basic information

• Entry: Database: SASBDB / ID: SASDAH5

Sample

Complex of Hfq with DsrA

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

• Biological species: Escherichia coli (E. coli)
• Citation: Journal: Nucleic Acids Res / Year: 2012; Title: Structural flexibility of RNA as molecular basis for Hfq chaperone function.; Authors: Euripedes de Almeida Ribeiro / Mads Beich-Frandsen / Petr V Konarev / Weifeng Shang / Branislav Vecerek / Georg Kontaxis / Hermann Hämmerle / Herwig Peterlik / Dmitri I Svergun / Udo Bläsi / Kristina Djinović-Carugo / ; Abstract: In enteric bacteria, many small regulatory RNAs (sRNAs) associate with the RNA chaperone host factor Q (Hfq) and often require the protein for regulation of target mRNAs. Previous studies suggested that the hexameric Escherichia coli Hfq (Hfq(Ec)) binds sRNAs on the proximal site, whereas the distal site has been implicated in Hfq-mRNA interactions. Employing a combination of small angle X-ray scattering, nuclear magnetic resonance and biochemical approaches, we report the structural analysis of a 1:1 complex of Hfq(Ec) with a 34-nt-long subsequence of a natural substrate sRNA, DsrA (DsrA(34)). This sRNA is involved in post-transcriptional regulation of the E. coli rpoS mRNA encoding the stationary phase sigma factor RpoS. The molecular envelopes of Hfq(Ec) in complex with DsrA(34) revealed an overall asymmetric shape of the complex in solution with the protein maintaining its doughnut-like structure, whereas the extended DsrA(34) is flexible and displays an ensemble of different spatial arrangements. These results are discussed in terms of a model, wherein the structural flexibility of RNA ligands bound to Hfq stochastically facilitates base pairing and provides the foundation for the RNA chaperone function inherent to Hfq.

Contact author

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

Models

• Model #117: ; Type: atomic / Software: Sasref / Chi-square value: 2.25; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Complex of Hfq with DsrA / Sample MW: 50.5 kDa / Specimen concentration: 2.30-9.40 / Entity id: 90 / 91
• 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

Entity #91

Name: Hfq_DsrA / Type: RNA / Description: RNA DsrA / Formula weight: 12 / Num. of mol.: 1
Sequence:

5GAAUUUUUU AAGUGCUUCU UGCUUAAGCA AGUUU3

Experimental information

• Beam: Instrument name: DORIS III X33 / City: Hamburg / 国: Germany / Shape: 0.6 / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.15 Å / Dist. spec. to detc.: 2.7 mm
• Detector: Name: Pilatus 1M-W / Pixsize x: 0.172 mm

Scan

Measurement date: Nov 16, 2010 / Storage temperature: 35 °C / Cell temperature: 35 °C / Exposure time: 15 sec. / Number of frames: 8 / Unit: 1/nm /

	Min	Max
Q	0.1138	6.0155

Distance distribution function P(R)

Sofotware P(R): GNOM 4.6 / Number of points: 431 /

	Min	Max
Q	0.1329	6.01
P(R) point	6	436
R	0	14.5

Result

D max: 14.5 / Type of curve: single_conc /

	Experimental	Porod
MW	50.5 kDa	-
Volume	-	210 nm3

	P(R)	Guinier
Forward scattering, I0	59	58
Radius of gyration, Rg	4.4 nm	4.3 nm