Crystal structure of the class V GTP-binding RNA aptamer bound to its ligand: GTP recognition by a topologically complex intermolecular G-quadruplex.

Stafflinger H, Neißner K, Bartsch S, Pichler AK, Bartosik K, Dhamotharan K, Abele R, Duchardt-Ferner E, Micura R, Schindelin H, Wöhnert J, Nucleic Acids Res 53(22) (2025) Europe PMC

SASDWH4 – Class V GTP aptamer

Class V GTP aptamer apo
MWexperimental 56 kDa
MWexpected 22 kDa
VPorod 99 nm3
log I(s) 5.40×10-1 5.40×10-2 5.40×10-3 5.40×10-4
Class V GTP aptamer apo small angle scattering data  s, nm-1
ln I(s)
Class V GTP aptamer apo Guinier plot ln 5.41×10-1 Rg: 3.3 nm 0 (3.3 nm)-2 s2
(sRg)2I(s)/I(0)
Class V GTP aptamer apo Kratky plot 1.104 0 √3 sRg
p(r)
Class V GTP aptamer apo pair distance distribution function Rg: 3.4 nm 0 Dmax: 15.3 nm

Data validation

There are no models related to this curve.

Synchrotron SAXS data from solutions of Class V GTP aptamer in 50 mM Bis-Tris, 50 mM KCl, 2 mM MgCl2, pH 6.5 were collected on the EMBL P12 beam line at PETRA III (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.123985 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.00 mg/ml was measured at 20°C. 40 successive 0.095 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.

Class V GTP aptamer apo
Mol. type   RNA
Organism   Escherichia coli
Olig. state   Unknown
Mon. MW   22.1 kDa
Sequence   FASTA