SASDDK5: Mammalian prion protein mRNA (PrP mRNA wild type) with KCl and py...

基本情報

• 登録情報: データベース: SASBDB / ID: SASDDK5

試料

Mammalian prion protein mRNA (PrP mRNA wild type) with KCl and pyridostatin (PDS)

• octo-repeat PrP mRNA (RNA), PrPmRNA, human PrP ORF

• 生物種: human PrP ORF
• 引用: ジャーナル: Sci Rep / 年: 2019; タイトル: Octa-repeat domain of the mammalian prion protein mRNA forms stable A-helical hairpin structure rather than G-quadruplexes.; 著者: Andreas Czech / Petr V Konarev / Ingrid Goebel / Dmitri I Svergun / Peter R Wills / Zoya Ignatova / ; 要旨: Misfolding and aggregation of prion protein (PrP) causes neurodegenerative diseases like Creutzfeldt-Jakob disease (CJD) and scrapie. Besides the consensus that spontaneous conversion of normal cellular PrP into misfolded and aggregating PrP is the central event in prion disease, an alternative hypothesis suggests the generation of pathological PrP by rare translational frameshifting events in the octa-repeat domain of the PrP mRNA. Ribosomal frameshifting most commonly relies on a slippery site and an adjacent stable RNA structure to stall translating ribosome. Hence, it is crucial to unravel the secondary structure of the octa-repeat domain of PrP mRNA. Each of the five octa-repeats contains a motif (GGCGGUGGUGGCUGGG) which alone in vitro forms a G-quadruplex. Since the propensity of mRNA to form secondary structure depends on the sequence context, we set to determine the structure of the complete octa-repeat region. We assessed the structure of full-length octa-repeat domain of PrP mRNA using dynamic light scattering (DLS), small angle X-ray scattering (SAXS), circular dichroism (CD) spectroscopy and selective 2'-hydroxyl acylation analysis by primer extension (SHAPE). Our data show that the PrP octa-repeat mRNA forms stable A-helical hairpins with no evidence of G-quadruplex structure even in the presence of G-quadruplex stabilizing agents.

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 #1894: ; タイプ: dummy / ソフトウェア: (5.0) / ダミー原子の半径: 7.50 A / カイ2乗値: 1.098 / P-value: 0.091063; 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: Mammalian prion protein mRNA (PrP mRNA wild type) with KCl and pyridostatin (PDS); 試料濃度: 0.50-4.00
• バッファ: 名称: 10 mM Tris buffer with 100 mM KCl and 1 mM PDS / pH: 7.5

要素 #1021

名称: PrPmRNA / タイプ: RNA / 記述: octo-repeat PrP mRNA / 分子量: 71.89 / 分子数: 2 / 由来: human PrP ORF
配列:

AACACUGGGG GCAGCCGAUA CCCGGGGCAG GGCAGCCCUG GAGGCAACCG CUACCCACCU CAGGGCGGUG GUGGCUGGGG GCAGCCUCAU GGUGGUGGCU GGGGGCAGCC UCAUGGUGGU GGCUGGGGGC AGCCCCAUGG UGGUGGCUGG GGACAGCCUC AUGGUGGUGG CUGGGGUCAA GGAGGUGGCA CCCACCUCAG GGCGGUGGUG GCUGGGGGCC

実験情報

• ビーム: 設備名称: PETRA III EMBL P12 / 地域: Hamburg / 国: Germany / 線源: X-ray synchrotron / 波長: 0.124 Å / スペクトロメータ・検出器間距離: 3.1 mm
• 検出器: 名称: Pilatus 2M

スキャン

タイトル: Mammalian prion protein mRNA (PrP mRNA wild type) with KCl and pyridostatin (PDS)
測定日: 2017年6月6日 / 保管温度: 20 °C / セル温度: 20 °C / 照射時間: 0.05 sec. / フレーム数: 20 / 単位: 1/nm /

	Min	Max
Q	0.1161	5.0327

距離分布関数 P(R)

ソフトウェア P(R): GNOM 4.6 / ポイント数: 400 /

	Min	Max
Q	0.1189	3.41
P(R) point	1	400
R	0	31

結果

カーブのタイプ: merged

	実験値	Standard	Standard error	Porod
分子量	170 kDa	170 kDa	30	200 kDa
体積	-	-	-	220 nm3

	P(R)	P(R) error	Guinier	Guinier error
前方散乱 I0	125100	2200	126949	1852
慣性半径, Rg	9.28 nm	0.07	9.07 nm	0.09

	Min	Max	Error
D	-	31	1
Guinier point	1	12	-