Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2

Custódio T, Das H, Sheward D, Hanke L, Pazicky S, Pieprzyk J, Sorgenfrei M, Schroer M, Gruzinov A, Jeffries C, Graewert M, Svergun D, Dobrev N, Remans K, Seeger M, McInerney G, Murrell B, Hällberg B, Löw C, Nature Communications 11(1) (2020) DOI

SASDJG4 – SARS-CoV-2 spike protein ACE2 receptor binding domain (RBD)

Spike glycoprotein (ACE2 receptor binding domain)
MWI(0) 33 kDa
MWexpected 29 kDa
VPorod 64 nm3
log I(s) 3.06×103 3.06×102 3.06×101 3.06×100
Spike glycoprotein (ACE2 receptor binding domain) small angle scattering data  s, nm-1
ln I(s)
Spike glycoprotein (ACE2 receptor binding domain) Guinier plot ln 3.06×103 Rg: 3.0 nm 0 (3.0 nm)-2 s2
(sRg)2I(s)/I(0)
Spike glycoprotein (ACE2 receptor binding domain) Kratky plot 1.104 0 √3 sRg
p(r)
Spike glycoprotein (ACE2 receptor binding domain) pair distance distribution function Rg: 3.1 nm 0 Dmax: 13.1 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Spike glycoprotein (ACE2 receptor binding domain) SASREF model
log I(s)
 s, nm-1
Synchrotron SAXS data from solutions of SARS-CoV-2 spike protein ACE2 receptor binding domain (RBD) in 25 mM Tris 100 mM NaCl, pH 7.5 were collected on the EMBL P12 beam line at the PETRA III storage ring (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 1.10 mg/ml was measured at 20°C. 10 successive 0.100 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.

Spike glycoprotein (ACE2 receptor binding domain) (RBD SARS-CoV-2)
Mol. type   Protein
Organism   Severe acute respiratory syndrome coronavirus 2
Olig. state   Monomer
Mon. MW   29.3 kDa
 
UniProt   P0DTC2 (319-566)
Sequence   FASTA