Semi-synthesis of TDP-43 reveals the effects of phosphorylation in N-terminal domain on self-association

Sasaki D, Tenda M, Sohma Y, Communications Chemistry 8(1) (2025) DOI

SASDV74 – Ser48-phosphorylated N-terminal domain of transactive response DNA-binding protein 43 (TDP-43)

TAR DNA-binding protein 43
MWexperimental 14 kDa
MWexpected 9 kDa
VPorod 15 nm3
log I(s) 1.03×10-2 1.03×10-3 1.03×10-4 1.03×10-5
TAR DNA-binding protein 43 small angle scattering data  s, nm-1
ln I(s)
TAR DNA-binding protein 43 Guinier plot ln 1.04×10-2 Rg: 1.4 nm 0 (1.4 nm)-2 s2
(sRg)2I(s)/I(0)
TAR DNA-binding protein 43 Kratky plot 1.104 0 √3 sRg
p(r)
TAR DNA-binding protein 43 pair distance distribution function Rg: 1.4 nm 0 Dmax: 4.3 nm

Data validation

Fits and models

log I(s)
 s, nm-1
TAR DNA-binding protein 43 DAMMIF model
TAR DNA-binding protein 43 DAMMIF model
log I(s)
 s, nm-1
TAR DNA-binding protein 43 OTHER model
Synchrotron in-line size exclusion chromatography (SEC)-SAXS data for solution of Ser48-phosphorylated N-terminal domain of TDP-43 in 50 mM Tris-HCl pH 8.5, 150 mM NaCl, 1 mM DTT and 3% glycerol were collected on the BL38B1 beam line at SPring-8 (Hyogo prefecture, Japan) using a PILATUS 3 S 2M detector at a sample-detector distance of 2.4 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). The SEC conditions were as follows; A 200 μL sample at a concentration of 9 mg/mL was injected onto a Superdex 75 Increase 10/300 column (GE) at 20°C and eluted at a flow rate of 0.3 mL/min. Successive 28 frames (3 sec exposure per frame) within the SEC elution peak were extracted and used for averaging. The data were normalized to the intensity of the transmitted beam and radially averaged. The scattering from the solvent background was subtracted.

The dummy atom models shown in this entry (DAM) represent: 1) Top: the minimised spatial alignment of several individual models that have undergone subsequent volume and bead-occupancy correction (DAMFILT model) and 2) Bottom: an individual DAM model example and corresponding fit to the data. The entire DAMMIF model cohort (20 individual models) are made available in the full entry zip archive.

TAR DNA-binding protein 43 (TDP-43)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   8.9 kDa
 
UniProt   Q13148 (1-80)
Sequence   FASTA