Extended disorder at the cell surface: the conformational landscape of the ectodomains of syndecans

Gondelaud F, Bouakil M, Le Fèvre A, Erica Miele A, Chirot F, Duclos B, Liwo A, Ricard-Blum S, Matrix Biology Plus :100081 (2021) DOI

SASDL89 – Ectodomain of human syndecan-3

Syndecan-3
MWexperimental 39 kDa
MWexpected 39 kDa
log I(s) 4.58×10-2 4.58×10-3 4.58×10-4 4.58×10-5
Syndecan-3 small angle scattering data  s, nm-1
ln I(s)
Syndecan-3 Guinier plot ln 4.59×10-2 Rg: 6.5 nm 0 (6.5 nm)-2 s2
(sRg)2I(s)/I(0)
Syndecan-3 Kratky plot 1.104 0 3 sRg

Data validation


Fits and models


log I(s)
 s, nm-1
Ectodomain of human syndecan-3 Rg histogram Rg, nm
Syndecan-3 EOM/RANCH model
Syndecan-3 EOM/RANCH model
Syndecan-3 EOM/RANCH model
Syndecan-3 EOM/RANCH model
Syndecan-3 EOM/RANCH model

Synchrotron SAXS data from solutions of Ectodomain of human syndecan-3 in 10 mM HEPES, 150 mM NaCl, pH 7.4 were collected on the SWING beam line at the SOLEIL storage ring (Saint-Aubin, France) using a Eiger 4M detector at a sample-detector distance of 2.1 m and at a wavelength of λ = 0.1033 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 50.00 μl sample at 14.6 mg/ml was injected at a 0.20 ml/min flow rate onto a GE Superdex 200 Increase 5/150 column at 20°C. 900 successive 0.990 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.

50 ul of the ectodomain of human syndecan-3 (14.6 mg/ml) were injected on a Superdex S200 Increase 5/150 GL (GE Healthcare) at a flow rate of 0.2 ml/min at 20°C. Experimental molecular weight has been determined by ESI-MS (and in solution by SEC-MALLS, estimated at 38.8 kDa). PED: https://proteinensemble.org/PED00187

Tags: idp PED
Syndecan-3 (SDC3)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   38.8 kDa
 
UniProt   O75056 (47-387)
Sequence   FASTA
 
PED ID   PED00187