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

基本情報

• 登録情報: データベース: SASBDB / ID: SASDAH5

試料

Complex of Hfq with DsrA

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

• 生物種: Escherichia coli (大腸菌)
• 引用: ジャーナル: Nucleic Acids Res / 年: 2012; タイトル: Structural flexibility of RNA as molecular basis for Hfq chaperone function.; 著者: 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 / ; 要旨: 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.

登録者

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

モデル

• モデル #117: ; タイプ: atomic / ソフトウェア: Sasref / カイ2乗値: 2.25; Omokage検索でこの集合体の類似形状データを探す (詳細)

試料

• 試料: 名称: Complex of Hfq with DsrA / Sample MW: 50.5 kDa / 試料濃度: 2.30-9.40 / Entity id: 90 / 91
• バッファ: 名称: 50 mM Tris-HCL / pH: 7.5 / 組成: 150 mM NaCl, 1.0 mM DTT

要素 #90

名称: Hfq / タイプ: protein / 記述: RNA chaperone Hfq / 分子量: 11.2 / 分子数: 6 / 由来: Escherichia coli
配列:

MAKGQSLQDP FLNALRRERV PVSIYLVNGI KLQGQIESFD QFVILLKNTV SQMVYKHAIS TVVPSRPVSH HSNNAGGGTS SNYHHGSSAQ NTSAQQDSEE TE

要素 #91

名称: Hfq_DsrA / タイプ: RNA / 記述: RNA DsrA / 分子量: 12 / 分子数: 1
配列:

5GAAUUUUUU AAGUGCUUCU UGCUUAAGCA AGUUU3

実験情報

• ビーム: 設備名称: DORIS III X33 / 地域: Hamburg / 国: Germany / 形状: 0.6 / 線源: X-ray synchrotron / 波長: 0.15 Å / スペクトロメータ・検出器間距離: 2.7 mm
• 検出器: 名称: Pilatus 1M-W / Pixsize x: 0.172 mm

スキャン

測定日: 2010年11月16日 / 保管温度: 35 °C / セル温度: 35 °C / 照射時間: 15 sec. / フレーム数: 8 / 単位: 1/nm /

	Min	Max
Q	0.1138	6.0155

距離分布関数 P(R)

ソフトウェア P(R): GNOM 4.6 / ポイント数: 431 /

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

結果

D max: 14.5 / カーブのタイプ: single_conc /

	実験値	Porod
分子量	50.5 kDa	-
体積	-	210 nm3

	P(R)	Guinier
前方散乱 I0	59	58
慣性半径, Rg	4.4 nm	4.3 nm