SAXS/SANS on a model DIS heterocomplex

Aldrex Munsayac.

SASDUU8 – HIV-1 DIS-C:DIS-Gk RNA heterocomplex

HIV-1 dimerization initiation site with a CCCCCC apical loop
HIV-1 DIS with a GGGGGG apical loop, UCU bulge, and 16 bp helical extension
MWexperimental 30 kDa
MWexpected 30 kDa
VPorod 40 nm3
log I(s) 3.37×10-2 3.37×10-3 3.37×10-4 3.37×10-5
HIV-1 dimerization initiation site with a CCCCCC apical loop HIV-1 DIS with a GGGGGG apical loop, UCU bulge, and 16 bp helical extension small angle scattering data  s, nm-1
ln I(s)
HIV-1 dimerization initiation site with a CCCCCC apical loop HIV-1 DIS with a GGGGGG apical loop, UCU bulge, and 16 bp helical extension Guinier plot ln 3.38×10-2 Rg: 3.5 nm 0 (3.5 nm)-2 s2
(sRg)2I(s)/I(0)
HIV-1 dimerization initiation site with a CCCCCC apical loop HIV-1 DIS with a GGGGGG apical loop, UCU bulge, and 16 bp helical extension Kratky plot 1.104 0 √3 sRg
p(r)
HIV-1 dimerization initiation site with a CCCCCC apical loop HIV-1 DIS with a GGGGGG apical loop, UCU bulge, and 16 bp helical extension pair distance distribution function Rg: 3.7 nm 0 Dmax: 13.5 nm

Data validation

Fits and models

log I(s)
 s, nm-1
HIV-1 dimerization initiation site with a CCCCCC apical loop HIV-1 DIS with a GGGGGG apical loop, UCU bulge, and 16 bp helical extension RNAMASONRY model
log I(s)
 s, nm-1
Synchrotron SAXS data from solutions of the HIV-1 DIS-C:DIS-Gk RNA heterocomplex in 50 mM potassium phosphate buffer, 1 mM MgCl2, 50 mM NaCl, pH 7.5 were collected on the BioCAT 18ID beam line at the Advanced Photon Source (APS), Argonne National Laboratory (Lemont, IL, USA) using a Eiger2 XE 9M (Dectris) detector at a sample-detector distance of 3.7 m and at a wavelength of λ = 0.1033 nm (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 250.00 μl sample at 3.4 mg/ml was injected at a 0.60 ml/min flow rate onto a GE Superdex 75 Increase 10/300 column at 20°C. 47 successive 0.500 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

HIV-1 dimerization initiation site with a CCCCCC apical loop (DIS-C)
Mol. type   RNA
Olig. state   Monomer
Mon. MW   9.3 kDa
Sequence   FASTA
 
HIV-1 DIS with a GGGGGG apical loop, UCU bulge, and 16 bp helical extension (DIS-Gk)
Mol. type   RNA
Olig. state   Monomer
Mon. MW   20.8 kDa
Sequence   FASTA