Encoded Conformational Dynamics of the HIV Splice Site A3 Regulatory Locus: Implications for Differential Binding of hnRNP Splicing Auxiliary Factors.

Chiu LY, Emery A, Jain N, Sugarman A, Kendrick N, Luo L, Ford W, Swanstrom R, Tolbert BS, J Mol Biol 434(18):167728 (2022) Europe PMC

SASDPD3 – Second exon splicing silencer 2p (ESS2p) RNA, apo

The second exon splicing silencer 2p
MWexperimental 13 kDa
MWexpected 14 kDa
VPorod 21 nm3
log I(s) 1.05×102 1.05×101 1.05×100 1.05×10-1
The second exon splicing silencer 2p small angle scattering data  s, nm-1
ln I(s)
The second exon splicing silencer 2p Guinier plot ln 1.06×102 Rg: 2.1 nm 0 (2.1 nm)-2 s2
(sRg)2I(s)/I(0)
The second exon splicing silencer 2p Kratky plot 1.104 0 √3 sRg
p(r)
The second exon splicing silencer 2p pair distance distribution function Rg: 2.2 nm 0 Dmax: 6.9 nm

Data validation

Fits and models

log I(s)
 s, nm-1
The second exon splicing silencer 2p AMBER model
Synchrotron SAXS data from solutions of the second exon splicing silencer 2p (ESS2p) RNA in 20 mM Bis-Tris, 20 mM NaCl, pH 6.2 were collected on the BioCAT 18ID beam line at the Advanced Photon Source (APS), Argonne National Laboratory (Lemont, IL, USA) using a MAR 165 CCD detector (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A sample was injected onto a column . The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

CAUTION: X-ray wavelength, unknown. CAUTION: Cell temperature/experimental temperature, unknown. CAUTION: Sample-to-detector distance, unknown. CAUTION: X-ray exposure time, unknown. CAUTION: sample concentration, unknown. CAUTION: SEC-column, unknown. CAUTION: SEC sample injection concentration, unknown. CAUTION: SEC flow rate, unknown.

The second exon splicing silencer 2p (ESS2p)
Mol. type   RNA
Olig. state   Monomer
Mon. MW   13.8 kDa
Sequence   FASTA