Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries.

Tsai YX, Chang NE, Reuter K, Chang HT, Yang TJ, von Bülow S, Sehrawat V, Zerrouki N, Tuffery M, Gecht M, Grothaus IL, Colombi Ciacchi L, Wang YS, Hsu MF, Khoo KH, Hummer G, Hsu SD, Hanus C, Sikora M, Cell 187(5):1296-1311.e26 (2024) Europe PMC

SASDT45 – N-cadherin extracellular domains EC4-EC5

Cadherin-2
MWexperimental 18 kDa
MWexpected 24 kDa
VPorod 63 nm3
log I(s) 1.27×10-2 1.27×10-3 1.27×10-4 1.27×10-5
Cadherin-2 small angle scattering data  s, nm-1
ln I(s)
Cadherin-2 Guinier plot ln 1.27×10-2 Rg: 3.4 nm 0 (3.4 nm)-2 s2
(sRg)2I(s)/I(0)
Cadherin-2 Kratky plot 1.104 0 √3 sRg
p(r)
Cadherin-2 pair distance distribution function Rg: 3.5 nm 0 Dmax: 12.6 nm

Data validation

There are no models related to this curve.

Synchrotron SAXS data from solutions of N-cadherin extracellular domains EC4-EC5 in 10 mM HEPES, 150 mM NaCl, 3 mM CaCl2, 0.02% NaN3, pH 8 were collected on the 13A beam line at the Taiwan Photon Source (NSRRC; Hsinchu, Taiwan) using a Eiger X 1M and Eiger X 9M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.0827 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 805.00 μl sample at 5 mg/ml was injected at a 0.10 ml/min flow rate onto a Agilent Bio SEC-3, 300 Å column at 13°C. Six successive 2 second frames were collected through the SEC sample peak. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

Possibly aggregated.

Cadherin-2 (N-cadherin EC4-EC5)
Mol. type   Protein
Organism   Mus musculus
Olig. state   Monomer
Mon. MW   24.3 kDa
 
UniProt   P15116 (490-702)
Sequence   FASTA