SASDDP5: Mutant mammalian prion protein mRNA (octo-repear PrP mRNA) with K...

Basic information

• Entry: Database: SASBDB / ID: SASDDP5

Sample

Mutant mammalian prion protein mRNA (octo-repear PrP mRNA) with KCl and pyridostatin (PDS)

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

• Biological species: human PrP ORF
• Citation: Journal: Sci Rep / Year: 2019; Title: Octa-repeat domain of the mammalian prion protein mRNA forms stable A-helical hairpin structure rather than G-quadruplexes.; Authors: Andreas Czech / Petr V Konarev / Ingrid Goebel / Dmitri I Svergun / Peter R Wills / Zoya Ignatova / ; Abstract: 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.

Contact author

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

Models

• Model #1898: ; Type: dummy / Software: (5.0) / Radius of dummy atoms: 7.75 A / Chi-square value: 1.131 / P-value: 0.000730; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Mutant mammalian prion protein mRNA (octo-repear PrP mRNA) with KCl and pyridostatin (PDS); Specimen concentration: 0.50-4.00
• Buffer: Name: 10 mM Tris buffer with 100 mM KCl and 1 mM PDS / pH: 7.5

Entity #1022

Name: PrPmRNA_mut / Type: RNA / Description: octo-repeat PrP mRNA mutant / Formula weight: 71.843 / Num. of mol.: 2 / Source: human PrP ORF
Sequence:

AACACUGGGG GCAGCCGAUA CCCGGGGCAG GGCAGCCCUG GAGGCAACCG CUACCCACCU CAGGGCGCUG CUGCCUGGGG GCAGCCUCAU GCUGCUGCCU GGGGGCAGCC UCAUGCUGCU GCCUGGGGGC AGCCCCAUGC UGCUGCCUGG GGACAGCCUC AUGCUGCUGC CUGGGGUCAA GGAGGUGGCA CCCACCUCAG GGCGCUGCUG CCUGGGGGCA GC

Experimental information

• Beam: Instrument name: PETRA III EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.124 Å / Dist. spec. to detc.: 3.1 mm
• Detector: Name: Pilatus 2M

Scan

Title: Mutant mammalian prion protein mRNA (octo-repear PrP mRNA) with KCl and pyridostatin (PDS)
Measurement date: Jun 6, 2017 / Storage temperature: 20 °C / Cell temperature: 20 °C / Exposure time: 0.05 sec. / Number of frames: 20 / Unit: 1/nm /

	Min	Max
Q	0.1161	5.0327

Distance distribution function P(R)

Sofotware P(R): GNOM 4.6 / Number of points: 400 /

	Min	Max
Q	0.1189	3.41
P(R) point	1	400
R	0	33

Result

Type of curve: merged

	Experimental	Standard	Standard error	Porod
MW	185 kDa	185 kDa	30	225 kDa
Volume	-	-	-	260 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	128000	2200	127428	1924
Radius of gyration, Rg	9.87 nm	0.15	9.23 nm	0.13

	Min	Max	Error
D	-	33	1
Guinier point	1	14	-