Dynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy.

Jadhav S, Maiorca M, Manigrasso J, Saha S, Rakitch A, Muscat S, Mulvaney T, De Vivo M, Topf M, Marcia M, Nat Commun 16(1):10195 (2025) Europe PMC

SASDX39 – Group IIC Intron Domain 1

Group IIC Intron Domain 1
MWexperimental 113 kDa
MWexpected 89 kDa
VPorod 188 nm3
log I(s) 2.36×101 2.36×100 2.36×10-1 2.36×10-2
Group IIC Intron Domain 1 small angle scattering data  s, nm-1
ln I(s)
Group IIC Intron Domain 1 Guinier plot ln 2.37×101 Rg: 3.8 nm 0 (3.8 nm)-2 s2
(sRg)2I(s)/I(0)
Group IIC Intron Domain 1 Kratky plot 1.104 0 √3 sRg
p(r)
Group IIC Intron Domain 1 pair distance distribution function Rg: 3.8 nm 0 Dmax: 13.0 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Group IIC Intron Domain 1 DAMMIF model
Synchrotron SAXS data from solutions of Group IIC Intron Domain 1 in 10 mM MgCl2, 5 mM Na-MES, pH 6.5 were collected on the BM29 beam line at the ESRF storage ring (Grenoble, France) using a Pilatus3 2M detector at a sample-detector distance of 2.8 m and at a wavelength of λ = 0.9918 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 95.00 μl sample at 1.1 mg/ml was injected at a 0.50 ml/min flow rate onto a column at 25°C. 1700 successive 2 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.

SEC column = UNKNOWN

Group IIC Intron Domain 1 (D1)
Mol. type   RNA
Organism   Oceanobacillus iheyensis
Olig. state   Monomer
Mon. MW   89 kDa
Sequence   FASTA