The Human RNA Helicase DDX21 Presents a Dimerization Interface Necessary for Helicase Activity

Marcaida M, Kauzlaric A, Duperrex A, Sülzle J, Moncrieffe M, Adebajo D, Manley S, Trono D, Dal Peraro M, iScience 23(12):101811 (2020) DOI

SASDGW9 – Nucleolar RNA helicase 2 (DDX21) fragment 186-710

Nucleolar RNA helicase 2 fragment 186-710
MWexperimental 122 kDa
MWexpected 121 kDa
VPorod 238 nm3
log I(s) 6.90×101 6.90×100 6.90×10-1 6.90×10-2
Nucleolar RNA helicase 2 fragment 186-710 small angle scattering data  s, nm-1
ln I(s)
Nucleolar RNA helicase 2 fragment 186-710 Guinier plot ln 6.90×101 Rg: 4.6 nm 0 (4.6 nm)-2 s2
(sRg)2I(s)/I(0)
Nucleolar RNA helicase 2 fragment 186-710 Kratky plot 1.104 0 √3 sRg
p(r)
Nucleolar RNA helicase 2 fragment 186-710 pair distance distribution function Rg: 4.7 nm 0 Dmax: 17.7 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Nucleolar RNA helicase 2 (DDX21) fragment 186-710 Rg histogram Rg, nm
log I(s)
 s, nm-1
Nucleolar RNA helicase 2 fragment 186-710 DAMMIF model
log I(s)
 s, nm-1
Nucleolar RNA helicase 2 fragment 186-710 SWISSMODEL model
log I(s)
 s, nm-1
Nucleolar RNA helicase 2 fragment 186-710 SWISSMODEL model
Synchrotron SAXS data from solutions of Nucleolar RNA helicase 2 (DDX21) fragment 186-710 in 20 mM HEPES, 500 mM NaCl, 10 % Glycerol, 2 mM TCEP, pH 7.5 were collected on the BM29 beam line at the ESRF storage ring (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.099 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 100.00 μl sample at 10 mg/ml was injected at a 0.50 ml/min flow rate onto a GE Superose 6 Increase 10/300 column at 20°C. 3000 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 results from ensemble optimization methos are included in the full entry zip archive. In addition, two atomistic models are shown. The first model (X^2 = 1.25) was built using two PDBs as templates in SwissModel (2M3D, 3I32). The N-terminal unstructured tags were added using I-TASSER and the model was submitted to nonlinear Cartesian Normal Mode Analysis (NOLB NMA) resulting in the final model. The second model (bottom) was created substituting the helicase domain of model 1) by the crystal structure of this domain (PDB 6l5n) and removing the His-tags.

Nucleolar RNA helicase 2 fragment 186-710 (DDX21 fragment 186-7)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Dimer
Mon. MW   60.6 kDa
 
UniProt   Q9NR30 (186-710)
Sequence   FASTA