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

SASDL99 – Ectodomain of human syndecan-4 isoform-2 Monomer

Syndecan-4
MWexperimental 18 kDa
MWexpected 18 kDa
log I(s) 2.06×10-2 2.06×10-3 2.06×10-4 2.06×10-5
Syndecan-4 small angle scattering data  s, nm-1
ln I(s)
Syndecan-4 Guinier plot ln 2.07×10-2 Rg: 4.2 nm 0 (4.2 nm)-2 s2
(sRg)2I(s)/I(0)
Syndecan-4 Kratky plot 1.104 0 3 sRg

Data validation


Fits and models


log I(s)
 s, nm-1
Ectodomain of human syndecan-4 isoform-2 Monomer Rg histogram Rg, nm
Syndecan-4 EOM/RANCH model
Syndecan-4 EOM/RANCH model
Syndecan-4 EOM/RANCH model
Syndecan-4 EOM/RANCH model
Syndecan-4 EOM/RANCH model
Syndecan-4 EOM/RANCH model
Syndecan-4 EOM/RANCH model
Syndecan-4 EOM/RANCH model
Syndecan-4 EOM/RANCH model

Synchrotron SAXS data from solutions of Ectodomain of human syndecan-4 isoform-2 Monomer 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 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 8.3 mg/ml was injected at a 0.20 ml/min flow rate onto a GE Superdex 200 Increase 5/150 column at 20°C. 600 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-4 isoform-2 (8.3 mg/ml, comprising a mix of monomers and dimers) 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 18.0 kDa). PED: https://proteinensemble.org/PED00188

Tags: idp PED
Syndecan-4 (SDC4)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   17.8 kDa
 
UniProt   P31431-2 (19-153)
Sequence   FASTA
 
PED ID   PED00188