A Simple Protocol for Visualization of RNA-Protein Complexes by Atomic Force Microscopy.

Tripepi A, Shakoor H, Klapetek P, Curr Protoc 5(1):e70084 (2025) Europe PMC

SASDUU5 – Human Double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 bound to 3'UTR fragment of ADP-ribosylation factor 1

Double-stranded RNA-binding protein Staufen homolog 1 (Δ1-177)
3'UTR fragment of ADP-ribosylation factor 1
MWexperimental 94 kDa
MWexpected 103 kDa
VPorod 129 nm3
log I(s) 7.98×10-1 7.98×10-2 7.98×10-3 7.98×10-4
Double-stranded RNA-binding protein Staufen homolog 1 (Δ1-177) 3'UTR fragment of ADP-ribosylation factor 1 small angle scattering data  s, nm-1
ln I(s)
Double-stranded RNA-binding protein Staufen homolog 1 (Δ1-177) 3'UTR fragment of ADP-ribosylation factor 1 Guinier plot ln 7.98×10-1 Rg: 4.9 nm 0 (4.9 nm)-2 s2
(sRg)2I(s)/I(0)
Double-stranded RNA-binding protein Staufen homolog 1 (Δ1-177) 3'UTR fragment of ADP-ribosylation factor 1 Kratky plot 1.104 0 3 sRg
p(r)
Double-stranded RNA-binding protein Staufen homolog 1 (Δ1-177) 3'UTR fragment of ADP-ribosylation factor 1 pair distance distribution function Rg: 4.6 nm 0 Dmax: 13.4 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Double-stranded RNA-binding protein Staufen homolog 1 (Δ1-177) 3'UTR fragment of ADP-ribosylation factor 1 CORAL model

SAXS data from solutions of double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 bound to the 3'UTR fragment of ADP-ribosylation factor 1 in 50 mM TRIS, 300 mM NaCl, 3.8 mM β-mercaptoethanol, pH 7 were collected using a Rigaku BioSAXS-1000 instrument at CEITEC (Brno, Czech Republic) equipped with a Pilatus 100K detector at a sample-detector distance of 0.5 m and at a wavelength of λ = 0.154 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 4.00 mg/ml was measured at 4°C. One 3600 second frame was collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

Double-stranded RNA-binding protein Staufen homolog 1 (Δ1-177) (Stau1_dsRBD3-end)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Dimer
Mon. MW   44.4 kDa
 
UniProt   O95793 (178-577)
Sequence   FASTA
 
3'UTR fragment of ADP-ribosylation factor 1 (ARF1)
Mol. type   RNA
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   14.2 kDa
Sequence   FASTA