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 Jan)
PMID: 39781608
doi: 10.1002/cpz1.70084 		Submitted to SASBDB: 2024 Mar 22
Published in SASBDB:

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 experimental SAS data
CORAL model
Sample: Double-stranded RNA-binding protein Staufen homolog 1 (Δ1-177) dimer, 89 kDa Homo sapiens protein
3'UTR fragment of ADP-ribosylation factor 1 monomer, 14 kDa Homo sapiens RNA
Buffer: 50 mM TRIS, 300 mM NaCl, 3.8 mM β-mercaptoethanol, pH: 7
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2020 May 4
RgGuinier 4.9 nm
Dmax 13.4 nm
VolumePorod 129 nm3

SASDUS5 – Human Double-stranded RNA-binding protein Staufen homolog 1

Double-stranded RNA-binding protein Staufen homolog 1 (Δ1-81) experimental SAS data
Human Double-stranded RNA-binding protein Staufen homolog 1 Rg histogram
Sample: Double-stranded RNA-binding protein Staufen homolog 1 (Δ1-81) dimer, 110 kDa Homo sapiens protein
Buffer: 50 mM TRIS, 300 mM NaCl, 3.8 mM β-mercaptoethanol, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Apr 23
RgGuinier 5.0 nm
Dmax 14.1 nm
VolumePorod 86 nm3

SASDUT5 – Human Double-stranded RNA-binding protein Staufen homolog 1 with truncated Staufen-swapping motif (ΔSSM) monomeric structures

Double-stranded RNA-binding protein Staufen homolog 1 with truncated Staufen-swapping motif (ΔSSM) experimental SAS data
Human Double-stranded RNA-binding protein Staufen homolog 1 with truncated Staufen-swapping motif (ΔSSM) monomeric structures Rg histogram
Sample: Double-stranded RNA-binding protein Staufen homolog 1 with truncated Staufen-swapping motif (ΔSSM) monomer, 52 kDa Homo sapiens protein
Buffer: 50 mM TRIS, 300 mM NaCl, 3.8 mM β-mercaptoethanol, pH: 7
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2020 May 4
RgGuinier 3.8 nm
Dmax 15.1 nm
VolumePorod 51 nm3

SASDUV5 – Human Double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 and truncated Staufen-swapping (ΔSSM) motif bound to 3'UTR fragment of ADP-ribosylation factor 1

3'UTR fragment of ADP-ribosylation factor 1Double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 and truncated Staufen-swapping (ΔSSM) experimental SAS data
CORAL model
Sample: 3'UTR fragment of ADP-ribosylation factor 1 monomer, 14 kDa Homo sapiens RNA
Double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 and truncated Staufen-swapping (ΔSSM) dimer, 81 kDa Homo sapiens protein
Buffer: 50 mM TRIS, 300 mM NaCl, 3.8 mM β-mercaptoethanol, pH: 7
Experiment: SAXS data collected at Rigaku BioSAXS-2000, CEITEC on 2024 Jan 12
RgGuinier 5.5 nm
Dmax 16.1 nm
VolumePorod 139 nm3