The dynamic nature of netrin-1 and the structural basis for glycosaminoglycan fragment-induced filament formation

Meier M, Gupta M, Akgül S, McDougall M, Imhof T, Nikodemus D, Reuten R, Moya-Torres A, To V, Ferens F, Heide F, Padilla-Meier G, Kukura P, Huang W, Gerisch B, Mörgelin M, Poole K, Antebi A, Koch M, Stetefeld J, Nature Communications 14(1) (2023) DOI

SASDRK2 – Chicken Netrin-1 ΔC dimer (experiment ID: sm22113-7/sample1)

MWexperimental 76 kDa
MWexpected 99 kDa
VPorod 145 nm3
log I(s) 1.05×100 1.05×10-1 1.05×10-2 1.05×10-3
Netrin-1 small angle scattering data  s, nm-1
ln I(s)
Netrin-1 Guinier plot ln 1.06×100 Rg: 5.9 nm 0 (5.9 nm)-2 s2
Netrin-1 Kratky plot 1.104 0 3 sRg
Netrin-1 pair distance distribution function Rg: 6.0 nm 0 Dmax: 21.3 nm

Data validation

Fits and models

log I(s)
 s, nm-1

log I(s)
 s, nm-1

log I(s)
 s, nm-1

SEC-SAXS data were collected at beamline B21, Diamond Light Source (Didcot, UK) that operates at a wavelength of 0.1 nm at a photon flux of ~10¹² photons per second and features a fixed camera length of 4.014 m. It is equipped with an Agilent 1200 HPLC system. Tag-free chicken Netrin-1 ΔC was shipped injection-ready to the beamline at 5.8 mg/ml in 20 mM tris, pH 7.5, 500 mM NaCl (sample1). 50 µl of sample was injected into a size exclusion column equilibrated with the respective buffer (matched to the sample by overnight dialysis). For sample1, we used a Shodex KW403-4F column with a flow rate of 0.16 ml/min. The elution traces were assessed with the program BioXTAS RAW which showed two overlapping peaks, indicating the presence of at least two different scattering components. Using the evolving factor analysis (EFA) implemented in BioXTAS RAW, we deconvoluted the scattering signals of the dimeric component.

Experiment ID: sm22113-7/sample1 (b21-403956). Additional modelling information, including log files, are provided in the full entry zip archive. Each respective fit displays two maps: 1) The refined averaged map (top) and; 2) The corresponding object support (bottom).

Netrin-1 (NET1 ΔC)
Mol. type   Protein
Organism   Gallus gallus
Olig. state   Dimer
Mon. MW   49.5 kDa
UniProt   Q90922 (26-458)
Sequence   FASTA