Medical contrast agents as promising tools for biomacromolecular SAXS experiments.

Gabel F, Engilberge S, Schmitt E, Thureau A, Mechulam Y, Pérez J, Girard E, Acta Crystallogr D Struct Biol 78(Pt 9):1120-1130 (2022) Europe PMC

SASDNP7 – Translation initiation factor 2 (aIF2)-tRNA complex in Gd-HPDO3A

Translation initiation factor 2 subunit gamma
Translation initiation factor 2 subunit alpha
transfer RNA
MWexperimental 80 kDa
MWexpected 79 kDa
VPorod 102 nm3
log I(s) 4.04×10-1 4.04×10-2 4.04×10-3 4.04×10-4
Translation initiation factor 2 subunit gamma Translation initiation factor 2 subunit alpha transfer RNA small angle scattering data  s, nm-1
ln I(s)
Translation initiation factor 2 subunit gamma Translation initiation factor 2 subunit alpha transfer RNA Guinier plot ln 4.05×10-1 Rg: 3.6 nm 0 (3.6 nm)-2 s2
(sRg)2I(s)/I(0)
Translation initiation factor 2 subunit gamma Translation initiation factor 2 subunit alpha transfer RNA Kratky plot 1.104 0 √3 sRg
Dmax: 13 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Translation initiation factor 2 subunit gamma Translation initiation factor 2 subunit alpha transfer RNA PDB (PROTEIN DATA BANK) model
Synchrotron SAXS data from solutions of an aIF2-tRNA complex in 10 mM MOPS-NaOH pH 6.7, 200 mM NaCl, 5 mM MgCl 2, 1 mM 5'-guanylyl imidodiphosphate (GDPNP) were collected on the SWING beam line at SOLEIL (Saint-Aubin, France) using a AVIEX PCCD170170 detector at a sample-detector distance of 1.8 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 1.65 mg/ml was measured at 15°C. 20 successive 1 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.

The data displayed in this entry is that of the aIF2-tRNA complex without the addition of Gd-HPDO3A that acts as X-ray contrast variation agent. Refer to the full entry zip archive that contains additional SAXS data and model fits in the presence of 464-1376 mM Gd-HPDO3A (https://pubchem.ncbi.nlm.nih.gov/compound/Gadoteridol).

Translation initiation factor 2 subunit gamma (aIF2-gamma)
Mol. type   Protein
Organism   Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
Olig. state   Monomer
Mon. MW   45.7 kDa
 
UniProt   Q980A5 (2-415)
Sequence   FASTA
 
Translation initiation factor 2 subunit alpha (aIF2-alpha)
Mol. type   Protein
Organism   Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
Olig. state   Monomer
Mon. MW   10.4 kDa
 
UniProt   Q97Z79
Sequence   FASTA
 
transfer RNA (tRNA)
Mol. type   RNA
Organism   Escherichia coli
Olig. state   Monomer
Mon. MW   23.3 kDa
Sequence   FASTA
 
PDB ID   3V11