The acidic intrinsically disordered region of the inflammatory mediator HMGB1 mediates fuzzy interactions with CXCL12.

Mantonico MV, De Leo F, Quilici G, Colley LS, De Marchis F, Crippa M, Mezzapelle R, Schulte T, Zucchelli C, Pastorello C, Carmeno C, Caprioglio F, Ricagno S, Giachin G, Ghitti M, Bianchi ME, Musco G, Nat Commun 15(1):1201 (2024) Europe PMC

SASDRG9 – Stromal cell-derived factor 1, CXCL12

Stromal cell-derived factor 1
MWexperimental 10 kDa
MWexpected 9 kDa
VPorod 19 nm3
log I(s) 3.26×101 3.26×100 3.26×10-1 3.26×10-2
Stromal cell-derived factor 1 small angle scattering data  s, nm-1
ln I(s)
Stromal cell-derived factor 1 Guinier plot ln 3.26×101 Rg: 1.5 nm 0 (1.5 nm)-2 s2
(sRg)2I(s)/I(0)
Stromal cell-derived factor 1 Kratky plot 1.104 0 √3 sRg
p(r)
Stromal cell-derived factor 1 pair distance distribution function Rg: 1.5 nm 0 Dmax: 4.8 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Stromal cell-derived factor 1 PDB (PROTEIN DATA BANK) model
Synchrotron SAXS data from solutions of CXCL12 in 20 mM Tris, 50 mM NaCl, pH 7.5 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus3 2M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.099 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.00 mg/ml was measured at 20°C. 10 successive 0.500 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.

Stromal cell-derived factor 1 (CXCL12)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   9.2 kDa
 
UniProt   P48061 (22-89)
Sequence   FASTA
 
PDB ID   2KEE