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 Mar 03)

doi: 10.1038/s41467-023-36692-w

Submitted to SASBDB: 2023 Jan 11 Published in SASBDB: 2023 Jan 13

SASDRJ2 – Chicken Netrin-1 ΔC monomer (experiment ID: sm22113-7/sample1) Sample: Netrin-1 monomer, 50 kDa Gallus gallus protein Buffer: 20 mM Tris-HCl, 500 mM NaCl, pH: 7.5 Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Oct 24 RgGuinier 4.0 nm Dmax 18.0 nm VolumePorod 103 nm3

SASDRK2 – Chicken Netrin-1 ΔC dimer (experiment ID: sm22113-7/sample1) Sample: Netrin-1 dimer, 99 kDa Gallus gallus protein Buffer: 20 mM Tris-HCl, 500 mM NaCl, pH: 7.5 Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Oct 24 RgGuinier 5.9 nm Dmax 21.3 nm VolumePorod 145 nm3

SASDRL2 – Chicken Netrin-1 ΔC monomer (experiment ID: sm22113-7/sample11) Sample: Netrin-1 monomer, 50 kDa Gallus gallus protein Buffer: 50 mM Tris-HCl, 200 mM NaCl, pH: 7.5 Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Oct 24 RgGuinier 4.1 nm Dmax 21.0 nm VolumePorod 84 nm3

SASDRM2 – Chicken Netrin-1 ΔC dimer (experiment ID: sm22113-7/sample11) Sample: Netrin-1 dimer, 99 kDa Gallus gallus protein Buffer: 50 mM Tris-HCl, 200 mM NaCl, pH: 7.5 Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Oct 24 RgGuinier 5.8 nm Dmax 23.0 nm VolumePorod 142 nm3

SASDRN2 – Chicken Netrin-1 ΔC bound to heparin oligosaccharide dp8 (experiment ID: sm16028-7/379532) Sample: Netrin-1 pentamer, 248 kDa Gallus gallus protein Heparin oligosaccharide dp8 ammonium salt monomer, 2 kDa Sus scrofa domesticus Buffer: 50 mM Tris-HCl, 200 mM NaCl, pH: 7.5 Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Nov 26 RgGuinier 6.5 nm Dmax 23.5 nm VolumePorod 729 nm3

SASDRP2 – Chicken Netrin-1 ΔC bound to heparin oligosaccharide dp8 (experiment ID: sm16028-7/379539) Sample: Netrin-1 pentamer, 248 kDa Gallus gallus protein Heparin oligosaccharide dp8 ammonium salt monomer, 2 kDa Sus scrofa domesticus Buffer: 50 mM Tris-HCl, 200 mM NaCl, pH: 7.5 Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Nov 26 RgGuinier 6.4 nm Dmax 21.9 nm VolumePorod 723 nm3

SASDRQ2 – Chicken Netrin-1 ΔC bound to heparin oligosaccharide dp10 (experiment ID: sm16028-7/379533) Sample: Netrin-1 pentamer, 248 kDa Gallus gallus protein Heparin oligosaccharide dp10 ammonium salt monomer, 3 kDa Sus scrofa domesticus Buffer: 50 mM Tris-HCl, 200 mM NaCl, pH: 7.5 Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Nov 26 RgGuinier 6.4 nm Dmax 21.7 nm VolumePorod 758 nm3

SASDRR2 – Chicken Netrin-1 ΔC bound to heparin oligosaccharide dp10 (experiment ID: sm16028-7/379540) Sample: Netrin-1 pentamer, 248 kDa Gallus gallus protein Heparin oligosaccharide dp10 ammonium salt monomer, 3 kDa Sus scrofa domesticus Buffer: 50 mM Tris-HCl, 200 mM NaCl, pH: 7.5 Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Nov 26 RgGuinier 6.5 nm Dmax 21.9 nm VolumePorod 769 nm3